General information
PDB ID 5FLX
Title MAMMALIAN 40S HCV-IRES COMPLEX
PDB header RIBOSOME
Date 2015-10-28
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.9
Kind rna
Organism ORYCTOLAGUS CUNICULUS, HEPATITIS C VIRUS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
PRIDB
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb5flx.pdb ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefg 1z 0
Biounits:
5flx.pdb1.pdb ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefg 1z 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Ribosomal_S5 Domain P15880_102-166 1.2e-32 1 CL0196 C 102 166 1   
Ribosomal_S5_C Domain P15880_185-256 2.1e-28 1 CL0329 C 185 256 1   
Ribosomal_S3_C Domain P23396_105-188 6.1e-23 1 No_clan D 105 188 1z   
KH_2 Domain P23396_20-96 2e-11 1 CL0007 D 20 96 1   
RS4NT Domain P22090_3-39 7.1e-22 1 No_clan E 3 39 1   
S4 Domain 0.00016 0 CL0492 E 42 90 1z
Ribosomal_S7 Domain P46782_51-204 2.8e-37 1 No_clan F 51 204 1z   
Ribosomal_S27 Domain P62979_102-147 1.2e-28 1 CL0167 f 102 147 1z   
S4 Domain P46781_108-154 3.8e-11 1 CL0492 J 108 154 1   
S10_plectin Domain P46783_3-97 5.4e-51 1 No_clan K 3 98 1   
Ribosomal_S17 Domain P62280_75-144 1.6e-29 1 CL0021 L 75 144 1   
Ribosomal_L7Ae Domain P25398_16-111 2.2e-30 1 CL0101 M 16 111 1   
Ribosomal_S13_N Domain P62277_2-60 2.2e-31 1 No_clan N 2 60 1   
Ribosomal_S15 Domain P62277_70-148 9e-16 1 CL0600 N 70 149 1   
Ribosomal_S19 Domain P62841_43-128 8.9e-41 1 No_clan P 43 128 1   
Ribosomal_S8 Domain P62244_5-130 2.1e-22 1 No_clan W 5 130 1   
Ribosomal_S26e Family P62854_2-102 1.6e-51 1 No_clan a 2 98 1z   
Ribosomal_S2 Family P08865_111-184 6.9e-13 1 CL0067 A 111 184 1   
Ribosomal_S2 Family P08865_18-118 3.6e-11 1 CL0067 A 18 118 1z   
40S_SA_C Family P08865_202-217 3.2e-05 1 No_clan A 202 219   
Ribosomal_S3Ae Family P61247_21-221 3.9e-106 1 No_clan B 22 221 1z   
Ribosomal_S27e Family P42677_28-82 1.2e-30 1 CL0167 b 28 82 1z   
Ribosomal_S28e Family P62857_8-68 1.1e-34 1 CL0021 c 7 67 1z   
Ribosomal_S14 Family P62273_6-55 1.9e-15 1 No_clan d 6 55 1   
Ribosomal_S4e Family P22090_95-169 1.2e-37 1 No_clan E 95 169 1   
Ribosomal_S30 Family P62861_4-58 3.1e-30 1 No_clan e 3 57 1z   
40S_S4_C Family P22090_212-258 1.1e-28 1 No_clan E 212 258 1   
KOW Family P22090_177-211 1.9e-05 1 CL0107 E 177 211 1   
Ribosomal_S6e Family P62753_1-126 7.6e-70 1 No_clan G 1 126 1   
Ribosomal_S7e Family P62081_8-191 2.9e-92 1 CL0652 H 12 191 1   
Ribosomal_S8e Family P62241_2-190 3.1e-62 1 No_clan I 2 190 1   
Ribosomal_S4 Family P46781_9-107 9.4e-06 1 CL0492 J 9 107 1   
Ribosomal_S17_N Family P62280_5-73 2.2e-36 1 No_clan L 6 73 1   
Ribosomal_S11 Family P62263_29-147 2.6e-47 1 CL0267 O 29 147 1z   
Ribosomal_S9 Family P62249_14-146 4.2e-34 1 CL0329 Q 14 146 1   
Ribosomal_S17e Family P08708_2-122 2.1e-69 1 No_clan R 2 119 1   
Ribosomal_S13 Family P62269_14-142 2.4e-56 1 CL0303 S 14 142 1   
Ribosomal_S19e Family P39019_5-141 1.4e-58 1 CL0123 T 5 141 1   
Ribosomal_S10 Family P60866_21-115 2.5e-31 1 No_clan U 21 115 1   
Ribosomal_S21e Family P63220_1-80 2.8e-43 1 No_clan V 1 80 1   
Ribosom_S12_S23 Family P62266_29-140 1.1e-51 1 CL0021 X 29 140 1   
Ribosomal_S24e Family P62847_24-102 5.3e-46 1 No_clan Y 24 102 1   
Ribosomal_S25 Family P62851_42-112 6e-38 1 CL0123 Z 41 112 1z   
WD40 Repeat P63244_224-260 6.8e-09 1 CL0186 g 95 133 1   
WD40 Repeat P63244_224-260 9.1e-09 1 CL0186 g 53 91 1   
WD40 Repeat P63244_224-260 3.6e-05 1 CL0186 g 136 178 1   
WD40 Repeat P63244_224-260 4.7e-05 1 CL0186 g 182 220 1   
WD40 Repeat P63244_224-260 0.00011 1 CL0186 g 224 260 1   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A=1-295 F laminin binding
A=1-295 F laminin receptor activity
A=1-295 F virus receptor activity
A=1-295 P cell adhesion
B=1-264 C nucleolus
B=1-264 C ribonucleoprotein complex
B=1-264 F mRNA 5'-UTR binding
B=1-264 P cell differentiation
B=1-264 P negative regulation of apoptotic process
b=1-84 F zinc ion binding
C=1-293 F cadherin binding
C=1-293 F enzyme binding
C=1-293 F fibroblast growth factor binding
C=1-293 F mRNA binding
C=1-293 P cellular response to interleukin-4
C=1-293 P positive regulation of ubiquitin-protein transferase activity
c=1-69 C cytoplasmic side of rough endoplasmic reticulum membrane
c=1-69 P maturation of SSU-rRNA
c=1-69 P ribosome biogenesis
D=1-243 C mitochondrial inner membrane
D=1-243 C mitochondrial matrix
D=1-243 C mitotic spindle
D=1-243 C NF-kappaB complex
D=1-243 C plasma membrane
D=1-243 C polysome
D=1-243 C ruffle membrane
D=1-243 F class I DNA-(apurinic or apyrimidinic site) endonuclease activity
D=1-243 F damaged DNA binding
D=1-243 F DNA-(apurinic or apyrimidinic site) endonuclease activity
D=1-243 F endodeoxyribonuclease activity
D=1-243 F Hsp70 protein binding
D=1-243 F Hsp90 protein binding
D=1-243 F iron-sulfur cluster binding
D=1-243 F kinase binding
D=1-243 F microtubule binding
D=1-243 F oxidized purine DNA binding
D=1-243 F oxidized pyrimidine DNA binding
D=1-243 F protein kinase A binding
D=1-243 F protein kinase binding
D=1-243 F protein-containing complex binding
D=1-243 F supercoiled DNA binding
D=1-243 F transcription factor binding
D=1-243 F tubulin binding
D=1-243 F ubiquitin-like protein conjugating enzyme binding
D=1-243 P apoptotic process
D=1-243 P cell division
D=1-243 P cellular response to DNA damage stimulus
D=1-243 P cellular response to hydrogen peroxide
D=1-243 P cellular response to reactive oxygen species
D=1-243 P cellular response to tumor necrosis factor
D=1-243 P chromosome segregation
D=1-243 P DNA damage response, detection of DNA damage
D=1-243 P DNA repair
D=1-243 P negative regulation of DNA repair
D=1-243 P negative regulation of protein ubiquitination
D=1-243 P positive regulation of activated T cell proliferation
D=1-243 P positive regulation of apoptotic signaling pathway
D=1-243 P positive regulation of base-excision repair
D=1-243 P positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis
D=1-243 P positive regulation of DNA N-glycosylase activity
D=1-243 P positive regulation of DNA repair
D=1-243 P positive regulation of endodeoxyribonuclease activity
D=1-243 P positive regulation of gene expression
D=1-243 P positive regulation of interleukin-2 production
D=1-243 P positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage
D=1-243 P positive regulation of JUN kinase activity
D=1-243 P positive regulation of microtubule polymerization
D=1-243 P positive regulation of NF-kappaB transcription factor activity
D=1-243 P positive regulation of NIK/NF-kappaB signaling
D=1-243 P positive regulation of T cell receptor signaling pathway
D=1-243 P regulation of apoptotic process
D=1-243 P response to TNF agonist
D=1-243 P spindle assembly
E=1-263 P multicellular organism development
e=1-59 C extracellular space
e=1-59 P antibacterial humoral response
e=1-59 P antimicrobial humoral immune response mediated by antimicrobial peptide
e=1-59 P defense response to Gram-positive bacterium
e=1-59 P innate immune response in mucosa
f=1-156 C endocytic vesicle membrane
f=1-156 C endoplasmic reticulum membrane
f=1-156 C endosome membrane
f=1-156 C host cell
f=1-156 C mitochondrial outer membrane
f=1-156 C vesicle
f=1-156 F metal ion binding
f=1-156 F protein tag
f=1-156 F ubiquitin protein ligase binding
f=1-156 P activation of MAPK activity
f=1-156 P anaphase-promoting complex-dependent catabolic process
f=1-156 P cellular protein metabolic process
f=1-156 P cytokine-mediated signaling pathway
f=1-156 P endosomal transport
f=1-156 P error-free translesion synthesis
f=1-156 P error-prone translesion synthesis
f=1-156 P global genome nucleotide-excision repair
f=1-156 P I-kappaB kinase/NF-kappaB signaling
f=1-156 P interleukin-1-mediated signaling pathway
f=1-156 P interstrand cross-link repair
f=1-156 P intracellular transport of virus
f=1-156 P JNK cascade
f=1-156 P membrane organization
f=1-156 P modification-dependent protein catabolic process
f=1-156 P MyD88-dependent toll-like receptor signaling pathway
f=1-156 P MyD88-independent toll-like receptor signaling pathway
f=1-156 P negative regulation of transforming growth factor beta receptor signaling pathway
f=1-156 P nucleotide-binding oligomerization domain containing signaling pathway
f=1-156 P nucleotide-excision repair, DNA damage recognition
f=1-156 P nucleotide-excision repair, DNA duplex unwinding
f=1-156 P nucleotide-excision repair, DNA gap filling
f=1-156 P nucleotide-excision repair, DNA incision
f=1-156 P nucleotide-excision repair, DNA incision, 5'-to lesion
f=1-156 P nucleotide-excision repair, preincision complex assembly
f=1-156 P positive regulation of transcription by RNA polymerase II
f=1-156 P protein deubiquitination
f=1-156 P protein polyubiquitination
f=1-156 P protein targeting to peroxisome
f=1-156 P regulation of mRNA stability
f=1-156 P regulation of transcription from RNA polymerase II promoter in response to hypoxia
f=1-156 P stress-activated MAPK cascade
f=1-156 P transcription-coupled nucleotide-excision repair
f=1-156 P transforming growth factor beta receptor signaling pathway
f=1-156 P translesion synthesis
f=1-156 P transmembrane transport
f=1-156 P TRIF-dependent toll-like receptor signaling pathway
f=1-156 P viral life cycle
f=1-156 P virion assembly
f=1-156 P Wnt signaling pathway
F=1-204 P regulation of translational fidelity
G=1-249 C cell body
G=1-249 C cytoplasmic ribonucleoprotein granule
G=1-249 P activation-induced cell death of T cells
G=1-249 P erythrocyte development
G=1-249 P G1/S transition of mitotic cell cycle
G=1-249 P glucose homeostasis
G=1-249 P mammalian oogenesis stage
G=1-249 P mitotic cell cycle checkpoint
G=1-249 P placenta development
G=1-249 P T cell differentiation in thymus
G=1-249 P T cell proliferation involved in immune response
G=1-249 P TOR signaling
g=1-317 C cytoplasm
g=1-317 C dendrite
g=1-317 C intracellular membrane-bounded organelle
g=1-317 C IRE1-RACK1-PP2A complex
g=1-317 C midbody
g=1-317 C mitochondrion
g=1-317 C neuronal cell body
g=1-317 C perikaryon
g=1-317 C perinuclear region of cytoplasm
g=1-317 C phagocytic cup
g=1-317 F BH3 domain binding
g=1-317 F cyclin binding
g=1-317 F cysteine-type endopeptidase activator activity involved in apoptotic process
g=1-317 F ion channel inhibitor activity
g=1-317 F molecular adaptor activity
g=1-317 F protein homodimerization activity
g=1-317 F protein kinase C binding
g=1-317 F protein phosphatase binding
g=1-317 F protein tyrosine kinase inhibitor activity
g=1-317 F receptor tyrosine kinase binding
g=1-317 F ribosome binding
g=1-317 F SH2 domain binding
g=1-317 F signaling adaptor activity
g=1-317 F signaling receptor binding
g=1-317 P activation of cysteine-type endopeptidase activity involved in apoptotic process
g=1-317 P cell cycle
g=1-317 P cellular response to glucose stimulus
g=1-317 P cellular response to growth factor stimulus
g=1-317 P gastrulation
g=1-317 P negative regulation of cell growth
g=1-317 P negative regulation of endoplasmic reticulum unfolded protein response
g=1-317 P negative regulation of gene expression
g=1-317 P negative regulation of hydrogen peroxide-induced neuron death
g=1-317 P negative regulation of peptidyl-serine phosphorylation
g=1-317 P negative regulation of phagocytosis
g=1-317 P negative regulation of protein binding
g=1-317 P negative regulation of protein kinase B signaling
g=1-317 P negative regulation of translation
g=1-317 P negative regulation of Wnt signaling pathway
g=1-317 P pigmentation
g=1-317 P positive regulation of apoptotic process
g=1-317 P positive regulation of cell migration
g=1-317 P positive regulation of ceramide biosynthetic process
g=1-317 P positive regulation of cyclic-nucleotide phosphodiesterase activity
g=1-317 P positive regulation of gastrulation
g=1-317 P positive regulation of Golgi to plasma membrane protein transport
g=1-317 P positive regulation of GTPase activity
g=1-317 P positive regulation of intrinsic apoptotic signaling pathway
g=1-317 P positive regulation of mitochondrial depolarization
g=1-317 P positive regulation of proteasomal ubiquitin-dependent protein catabolic process
g=1-317 P positive regulation of protein phosphorylation
g=1-317 P positive regulation of protein-containing complex assembly
g=1-317 P protein ubiquitination
g=1-317 P regulation of cell cycle
g=1-317 P regulation of cell division
g=1-317 P regulation of establishment of cell polarity
g=1-317 P regulation of protein localization
g=1-317 P regulation of tumor necrosis factor-mediated signaling pathway
g=1-317 P rescue of stalled ribosome
g=1-317 P rhythmic process
g=1-317 P viral process
H=1-194 C microtubule organizing center
H=1-194 C protein-containing complex
H=1-194 C small-subunit processome
H=1-194 F mRNA 3'-UTR binding
H=1-194 F ubiquitin ligase inhibitor activity
H=1-194 P negative regulation of ubiquitin protein ligase activity
H=1-194 P negative regulation of ubiquitin-dependent protein catabolic process
H=1-194 P positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator
H=1-194 P protein stabilization
I=1-208 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
J=1-194 F translation regulator activity
J=1-194 P positive regulation of cell population proliferation
J=1-194 P positive regulation of translational fidelity
M=1-132 C Golgi apparatus
N=1-151 C postsynaptic density
N=1-151 F small ribosomal subunit rRNA binding
N=1-151 P negative regulation of RNA splicing
O=1-151 P erythrocyte differentiation
O=1-151 P negative regulation of transcription by RNA polymerase II
P=1-145 C cytosol
P=1-145 C cytosolic small ribosomal subunit
P=1-145 C focal adhesion
P=1-145 C membrane
P=1-145 C nucleoplasm
P=1-145 C nucleus
P=1-145 F DNA binding
P=1-145 F RNA binding
P=1-145 F structural constituent of ribosome
P=1-145 P nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
P=1-145 P osteoblast differentiation
P=1-145 P ribosomal small subunit assembly
P=1-145 P ribosomal small subunit biogenesis
P=1-145 P ribosomal small subunit export from nucleus
P=1-145 P rRNA processing
P=1-145 P SRP-dependent cotranslational protein targeting to membrane
P=1-145 P translation
P=1-145 P translational initiation
P=1-145 P viral transcription
R=1-135 C ribosome
R=1-135 P erythrocyte homeostasis
S=1-152 C extracellular exosome
S=1-152 C small ribosomal subunit
S=1-152 C synapse
S=1-152 F rRNA binding
T=1-145 F identical protein binding
T=1-145 P defense response to Gram-negative bacterium
T=1-145 P killing of cells of other organism
T=1-145 P monocyte chemotaxis
T=1-145 P negative regulation of respiratory burst involved in inflammatory response
T=1-145 P Notch signaling pathway
T=1-145 P nucleolus organization
T=1-145 P positive regulation of cellular component movement
T=1-145 P positive regulation of respiratory burst involved in inflammatory response
T=1-145 P response to extracellular stimulus
V=1-83 F protein N-terminus binding
V=1-83 P endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
V=1-83 P endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
W=1-130 P positive regulation of cell cycle
W=1-130 P response to virus
X=1-143 C endoplasmic reticulum
X=1-143 C polysomal ribosome
X=1-143 C rough endoplasmic reticulum
X=1-143 P cytoplasmic translation
X=1-143 P maintenance of translational fidelity
X=1-143 P stress granule assembly
Y=1-133 F translation initiation factor binding
Sequences
Download file with secondary structure created by Stride  
5flx.pdb1.pdb:   [ download sequences in FASTA format ]
a (protein): 
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b (protein): 
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c (protein): 
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d (protein): 
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E (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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I (protein): 
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J (protein): 
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K (protein): 
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L (protein): 
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M (protein): 
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N (protein): 
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O (protein): 
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P (protein): 
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Q (protein): 
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R (protein): 
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S (protein): 
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T (protein): 
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U (protein): 
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V (protein): 
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W (protein): 
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X (protein): 
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Y (protein): 
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Z (protein): 
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1 (rna): 
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