General information
PDB ID 3J81
Title CRYOEM STRUCTURE OF A PARTIAL YEAST 48S PREINITIATION COMPLEX
PDB header RIBOSOME
Date 2014-08-29
Experimental method ELECTRON MICROSCOPY
Resolution (A) 4
Kind rna
Organism KLUYVEROMYCES LACTIS, SACCHAROMYCES CEREVISIAE, SYNTHETIC CONSTRUCT
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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:
pdb3j81.pdb ABCDEFGHIJKLMNOPQRSTUVWXYZabcfgdehijmkl 213 0
Biounits:
3j81.pdb1.pdb ABCDEFGHIJKLMNOPQRSTUVWXYZabcfgdehijmkl 213 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Ribosomal_S5 Domain Q6CKL3_81-145 6.9e-26 1 CL0196 C 81 145 23   
Ribosomal_S5_C Domain Q6CKL3_165-238 1.2e-22 1 CL0329 C 165 238 2   
Ribosomal_S3_C Domain Q6CRK7_105-188 1.5e-22 1 No_clan D 105 188 23   
KH_2 Domain Q6CRK7_20-96 2.9e-11 1 CL0007 D 20 96 2   
RS4NT Domain Q6CWJ2_3-39 2.9e-19 1 No_clan E 3 39 2   
S4 Domain Q6CWJ2_42-90 4.8e-08 1 CL0492 E 42 90 2   
Ribosomal_S7 Domain Q6CRA3_74-227 5.6e-37 1 No_clan F 74 227 23   
Ribosomal_S27 Domain P69061_102-145 4.1e-26 1 CL0167 f 102 145 2   
eIF-1a Domain P38912_32-94 6.7e-21 1 CL0021 i 32 94 23   
S1 Domain P20459_13-88 2.3e-14 1 CL0021 j 13 88 123   
S4 Domain Q6CM18_107-153 8.8e-13 1 CL0492 J 107 153 12   
S10_plectin Domain Q6CVZ5_3-95 1.4e-41 1 CL0123 K 3 95 2   
eIF2_C Domain P32481_428-517 1.1e-33 1 No_clan k 428 517   
GTP_EFTU Domain P32481_98-304 7.7e-21 1 CL0023 k 98 304   
GTP_EFTU_D2 Domain P32481_339-418 1.7e-06 0 CL0575 k 321 422 1   
Ribosomal_S17 Domain 1.6e-27 1 CL0021 L 73 141 2
SUI1 Domain P32911_23-99 5.5e-28 1 No_clan m 22 99 12   
Ribosomal_L7Ae Domain Q6CLU4_19-114 1.3e-18 1 CL0101 M 19 114 12   
Ribosomal_S13_N Domain Q6CJK0_2-60 6.4e-26 1 No_clan N 2 60 2   
Ribosomal_S15 Domain Q6CJK0_70-149 1.7e-13 1 CL0600 N 70 149 2   
Ribosomal_S19 Domain Q6CKV4_43-128 3e-33 1 No_clan P 43 128 2   
Ribosomal_S10 Domain Q6CIM1_20-114 5.9e-24 1 No_clan U 23 117 2   
Ribosomal_S8 Domain Q6CW21_5-130 4.2e-23 1 No_clan W 5 130 2   
Ribosomal_S26e Family Q6CS01_2-98 3.4e-48 1 No_clan a 2 98 23   
Ribosomal_S2 Family Q6CN12_110-183 2e-12 1 CL0067 A 110 183 2   
Ribosomal_S2 Family Q6CN12_17-116 2.2e-08 1 CL0067 A 17 116 23   
Ribosomal_S3Ae Family Q6CWD0_20-221 1.9e-78 1 No_clan B 19 221 2   
Ribosomal_S27e Family Q6CNL2_28-82 2.1e-29 1 CL0167 b 28 82 2   
Ribosomal_S28e Family P33285_5-66 6.2e-32 1 CL0021 c 6 66 23   
Ribosomal_S14 Family Q6CPG3_6-56 2.3e-14 1 No_clan d 6 56 2   
Ribosomal_S4e Family Q6CWJ2_95-169 6.3e-37 1 CL0021 E 95 169 2   
Ribosomal_S30 Family Q6CUH5_9-61 4.2e-26 1 No_clan e 8 61 2   
40S_S4_C Family Q6CWJ2_212-259 6.1e-25 1 No_clan E 212 259 2   
KOW Family Q6CWJ2_177-211 4.5e-06 1 CL0107 E 177 211 2   
Ribosomal_S6e Family Q6CM04_1-126 5.7e-55 1 No_clan G 1 126 2   
Ribosomal_S7e Family Q6CTD6_5-185 5.5e-78 1 CL0652 H 5 185 2   
Ribosomal_L41 Family P0CX86_1-25 1.4e-10 1 CL0652 h 1 25 2   
Ribosomal_S8e Family Q6CMG3_5-185 3.8e-56 1 No_clan I 5 185 123   
EIF_2_alpha Family P20459_126-237 3.5e-30 1 No_clan j 126 237 12   
Ribosomal_S4 Family Q6CM18_2-128 0.00022 1 CL0492 J 3 106 123   
Ribosomal_S17_N Family Q6CX80_8-71 1.5e-32 1 No_clan L 8 71 2   
Ribosomal_S11 Family P27069_15-133 4.4e-46 1 CL0267 O 15 133 2   
Ribosomal_S9 Family Q875N2_11-143 1.2e-32 1 CL0329 Q 11 143 12   
Ribosomal_S17e Family Q6CWU3_2-126 4.2e-54 1 No_clan R 2 126 2   
Ribosomal_S13 Family Q6CWT9_16-144 4.6e-57 1 CL0303 S 16 144 2   
Ribosomal_S19e Family Q6CXM0_5-142 1.5e-52 1 CL0123 T 5 142 2   
Ribosomal_S21e Family Q6CXT6_1-80 3.7e-40 1 No_clan V 1 80 2   
Ribosom_S12_S23 Family F2Z602_31-144 1.6e-51 1 CL0021 X 31 144 2   
Ribosomal_S24e Family Q6CU44_24-103 1.8e-34 1 No_clan Y 24 103 2   
Ribosomal_S25 Family Q6CW78_36-104 4.3e-26 1 CL0123 Z 36 104 2   
WD40 Repeat Q6CNI7_9-47 1.5e-08 1 CL0186 g 56 94 2   
WD40 Repeat Q6CNI7_9-47 7.9e-06 1 CL0186 g 98 136 2   
WD40 Repeat Q6CNI7_9-47 2.6e-05 1 CL0186 g 193 231 2   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A=1-254 C cytosolic small ribosomal subunit
A=1-254 F structural constituent of ribosome
A=1-254 P ribosomal small subunit assembly
A=1-254 P translation
B=1-255 C cytosolic small ribosomal subunit
B=1-255 F structural constituent of ribosome
B=1-255 P translation
c=1-67 C cytosolic small ribosomal subunit
c=1-67 F structural constituent of ribosome
c=1-67 P positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
c=1-67 P rRNA export from nucleus
c=1-67 P translation
d=1-56 C ribosome
d=1-56 F structural constituent of ribosome
d=1-56 F zinc ion binding
d=1-56 P translation
f=1-150 C cytosolic small ribosomal subunit
f=1-150 C nucleus
f=1-150 F metal ion binding
f=1-150 F protein tag
f=1-150 F structural constituent of ribosome
f=1-150 P maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S)
f=1-150 P ribosomal small subunit assembly
f=1-150 P translation
G=1-236 C ribosome
G=1-236 F structural constituent of ribosome
G=1-236 P translation
h=1-25 C cytosolic large ribosomal subunit
h=1-25 F structural constituent of ribosome
h=1-25 P cytoplasmic translation
i=1-153 C cytoplasmic stress granule
i=1-153 C eukaryotic 43S preinitiation complex
i=1-153 C eukaryotic 48S preinitiation complex
i=1-153 F double-stranded RNA binding
i=1-153 F protein kinase binding
i=1-153 F ribosomal small subunit binding
i=1-153 F translation initiation factor activity
i=1-153 F translation initiation factor binding
i=1-153 P formation of cytoplasmic translation initiation complex
i=1-153 P formation of translation initiation ternary complex
i=1-153 P formation of translation preinitiation complex
i=1-153 P translation reinitiation
j=1-300 C cytoplasm
j=1-300 C cytoplasmic stress granule
j=1-300 C eukaryotic 48S preinitiation complex
j=1-300 C eukaryotic translation initiation factor 2 complex
j=1-300 C eukaryotic translation initiation factor 2B complex
j=1-300 C multi-eIF complex
j=1-300 F ribosome binding
j=1-300 F RNA binding
j=1-300 F translation initiation factor activity
j=1-300 P formation of translation preinitiation complex
k=1-527 C cytoplasm
k=1-527 C cytosol
k=1-527 C eukaryotic 43S preinitiation complex
k=1-527 C eukaryotic 48S preinitiation complex
k=1-527 C eukaryotic translation initiation factor 2 complex
k=1-527 C multi-eIF complex
k=1-527 F GTP binding
k=1-527 F GTPase activity
k=1-527 F translation initiation factor activity
k=1-527 F translation initiation factor binding
k=1-527 P formation of translation preinitiation complex
k=1-527 P positive regulation of translational fidelity
k=1-527 P translational initiation
l=1-285 C eukaryotic 43S preinitiation complex
l=1-285 C eukaryotic translation initiation factor 2 complex
l=1-285 C multi-eIF complex
l=1-285 F metal ion binding
l=1-285 F mRNA binding
l=1-285 F translation initiation factor activity
l=1-285 F translation initiation factor binding
l=1-285 P formation of cytoplasmic translation initiation complex
l=1-285 P formation of translation preinitiation complex
m=1-108 C eukaryotic 43S preinitiation complex
m=1-108 C multi-eIF complex
m=1-108 F ribosomal small subunit binding
m=1-108 F RNA binding
m=1-108 F translation initiation factor activity
m=1-108 F translation initiation factor binding
m=1-108 P formation of translation preinitiation complex
m=1-108 P maintenance of translational fidelity
m=1-108 P regulation of translational fidelity
O=1-137 C ribosome
O=1-137 F structural constituent of ribosome
O=1-137 P translation
Q=1-143 C ribosome
Q=1-143 F structural constituent of ribosome
Q=1-143 P translation
V=1-87 C cytoplasm
V=1-87 C ribosome
V=1-87 F structural constituent of ribosome
V=1-87 P rRNA processing
V=1-87 P translation
W=1-130 C ribosome
W=1-130 F structural constituent of ribosome
W=1-130 P translation
Sequences
Download file with secondary structure created by Stride  
3j81.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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2 (rna): 
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3 (rna): 
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