General information
PDB ID 3JAP
Title STRUCTURE OF A PARTIAL YEAST 48S PREINITIATION COMPLEX IN CLOSED CONFORMATION
PDB header TRANSLATION
Date 2015-06-18
Experimental method ELECTRON MICROSCOPY
Resolution (A) 4.9
Kind rna
Organism KLUYVEROMYCES LACTIS, SYNTHETIC CONSTRUCT, SACCHAROMYCES CEREVISIAE
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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:
pdb3jap.pdb ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmopqrs 123 0
Biounits:
3jap.pdb1.pdb ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmopqrs 123 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 9.4e-27 1 CL0196 C 81 145 2   
Ribosomal_S5_C Domain Q6CKL3_164-235 1.3e-23 1 CL0329 C 164 235 2   
Ribosomal_S3_C Domain Q6CRK7_105-188 2.9e-22 1 No_clan D 105 188 2   
KH_2 Domain Q6CRK7_20-96 3.4e-11 1 CL0007 D 20 96 2   
RS4NT Domain Q6CWJ2_3-39 2.4e-20 1 No_clan E 3 39 2   
S4 Domain Q6CWJ2_42-90 3.7e-08 1 CL0492 E 42 90 2   
Ribosomal_S7 Domain Q6CRA3_74-227 1.7e-36 1 No_clan F 74 227 23   
Ribosomal_S27 Domain P69061_102-145 8.4e-26 1 CL0167 f 102 145 2   
eIF-1a Domain P38912_32-94 2.5e-20 1 CL0021 i 32 94 2   
S1 Domain P20459_13-88 1.6e-14 1 CL0021 j 13 88 12   
S4 Domain Q6CM18_107-153 7.7e-13 1 CL0492 J 107 153 12   
S10_plectin Domain Q6CVZ5_3-95 7.9e-42 1 No_clan K 3 95 2   
eIF2_C Domain P32481_428-517 1.5e-35 1 No_clan k 428 517   
GTP_EFTU Domain P32481_98-304 2.5e-23 1 CL0023 k 98 304 1   
GTP_EFTU_D2 Domain P32481_339-418 3.2e-11 1 CL0575 k 335 418 1   
Ribosomal_S17 Domain Q6CX80_73-141 8.3e-28 1 CL0021 L 73 141 2   
SUI1 Domain P32911_23-99 3.8e-27 1 No_clan m 22 99 12   
Ribosomal_L7Ae Domain Q6CLU4_19-114 2.2e-18 1 CL0101 M 19 114 12   
Ribosomal_S13_N Domain Q6CJK0_2-60 1.5e-26 1 No_clan N 2 60 2   
Ribosomal_S15 Domain Q6CJK0_70-149 1.4e-15 1 CL0600 N 70 149 2   
PCI Domain P27069_350-455 3e-05 1 CL0123 o 382 493   
Ribosomal_S19 Domain Q6CKV4_43-128 1.7e-34 1 No_clan P 43 128 2   
PCI Domain P32497_650-780 1.8e-14 1 CL0123 p 650 780   
Ribosomal_S8 Domain Q6CW21_5-130 1.4e-23 1 No_clan W 5 130 2   
Ribosomal_S26e Family Q6CS01_2-98 2.1e-48 1 No_clan a 2 99 23   
Ribosomal_S2 Family Q6CN12_110-183 2.2e-13 1 CL0067 A 111 183 2   
Ribosomal_S2 Family Q6CN12_17-117 2.9e-09 1 CL0067 A 17 116 23   
Ribosomal_S3Ae Family Q6CWD0_20-221 9e-90 1 No_clan B 5 221 2   
Ribosomal_S27e Family Q6CNL2_28-82 1.9e-29 1 CL0167 b 28 82 2   
Ribosomal_S28e Family P33285_5-66 1.1e-32 1 CL0021 c 6 66 2   
Ribosomal_S14 Family Q6CPG3_6-56 2.6e-14 1 No_clan d 6 56 2   
Ribosomal_S4e Family Q6CWJ2_95-169 1.1e-37 1 No_clan E 95 169 2   
Ribosomal_S30 Family Q6CUH5_9-61 9.7e-26 1 No_clan e 8 61 2   
40S_S4_C Family Q6CWJ2_212-259 9.3e-25 1 No_clan E 212 259 2   
KOW Family Q6CWJ2_177-211 4.9e-06 1 CL0107 E 177 211 2   
Ribosomal_S6e Family Q6CM04_1-126 2e-58 1 No_clan G 1 126 2   
Ribosomal_S7e Family Q6CTD6_5-187 4.1e-79 1 CL0652 H 5 187 2   
Ribosomal_L41 Family P0CX86_1-25 1.2e-10 1 CL0652 h 1 25 2   
Ribosomal_S8e Family Q6CMG3_2-185 2e-57 1 No_clan I 2 185 123   
EIF_2_alpha Family P20459_126-237 1.7e-27 1 No_clan j 126 237 12   
Ribosomal_S4 Family Q6CM18_2-128 9.1e-05 1 CL0492 J 3 128 12   
eIF-5_eIF-2B Family P09064_157-265 1.3e-38 1 No_clan l 140 265 12   
Ribosomal_S17_N Family Q6CX80_8-71 9.6e-33 1 No_clan L 8 71 2   
Ribosomal_S11 Family P27069_15-133 3.9e-46 1 CL0267 O 15 133 2   
eIF-3c_N Family P32497_251-640 5.2e-159 1 No_clan p 212 640 2   
Ribosomal_S9 Family Q875N2_11-143 1.6e-32 1 CL0329 Q 11 143 12   
Ribosomal_S17e Family Q6CWU3_2-126 5.1e-54 1 No_clan R 2 122 2   
Ribosomal_S13 Family Q6CWT9_16-144 4e-57 1 CL0303 S 16 144 2   
eIF3g Family A6ZZ25_45-96 3.9e-12 1 CL0511 s 45 96 2   
Ribosomal_S19e Family Q6CXM0_5-142 2.3e-53 1 CL0123 T 5 142 2   
Ribosomal_S10 Family Q6CIM1_20-114 4.1e-24 1 No_clan U 23 117 2   
Ribosomal_S21e Family Q6CXT6_1-80 4.1e-40 1 No_clan V 1 80 2   
Ribosom_S12_S23 Family F2Z602_31-144 1.4e-51 1 CL0021 X 31 144 2   
Ribosomal_S24e Family Q6CU44_24-102 1.7e-35 1 No_clan Y 24 102 2   
Ribosomal_S25 Family Q6CW78_36-104 1.1e-24 1 CL0123 Z 36 104 2   
WD40 Repeat Q6CNI7_194-231 1.3e-08 1 CL0186 g 56 94 2   
WD40 Repeat Q6CNI7_286-321 7e-06 1 CL0186 g 98 136 2   
WD40 Repeat Q6CNI7_286-321 2.3e-05 1 CL0186 g 193 231 2   
WD40 Repeat P40217_42-80 2.6e-05 1 CL0186 q 42 80 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=1-304 C cytoplasm
j=1-304 C cytoplasmic stress granule
j=1-304 C eukaryotic 48S preinitiation complex
j=1-304 C eukaryotic translation initiation factor 2 complex
j=1-304 C eukaryotic translation initiation factor 2B complex
j=1-304 C multi-eIF complex
j=1-304 F ribosome binding
j=1-304 F RNA binding
j=1-304 F translation initiation factor activity
j=1-304 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
o=1-495 C cytoplasm
o=1-495 C cytoplasmic stress granule
o=1-495 C eukaryotic 43S preinitiation complex
o=1-495 C eukaryotic 48S preinitiation complex
o=1-495 C eukaryotic translation initiation factor 3 complex
o=1-495 C eukaryotic translation initiation factor 3 complex, eIF3e
o=1-495 C eukaryotic translation initiation factor 3 complex, eIF3m
o=1-495 C incipient cellular bud site
o=1-495 C multi-eIF complex
o=1-495 F mRNA binding
o=1-495 F translation initiation factor activity
o=1-495 P formation of cytoplasmic translation initiation complex
o=1-495 P translation reinitiation
o=1-495 P translational initiation
p=193-812 C cytoplasm
p=193-812 C cytoplasmic stress granule
p=193-812 C eukaryotic 43S preinitiation complex
p=193-812 C eukaryotic 48S preinitiation complex
p=193-812 C eukaryotic translation initiation factor 3 complex
p=193-812 C multi-eIF complex
p=193-812 F mRNA binding
p=193-812 F translation initiation factor activity
p=193-812 F translation initiation factor binding
p=193-812 P formation of cytoplasmic translation initiation complex
p=193-812 P translational initiation
Q=1-143 C ribosome
Q=1-143 F structural constituent of ribosome
Q=1-143 P translation
q=1-347 C cytoplasmic stress granule
q=1-347 C eukaryotic 43S preinitiation complex
q=1-347 C eukaryotic 48S preinitiation complex
q=1-347 C eukaryotic translation initiation factor 3 complex
q=1-347 C eukaryotic translation initiation factor 3 complex, eIF3m
q=1-347 C multi-eIF complex
q=1-347 F RNA binding
q=1-347 F translation initiation factor activity
q=1-347 P cytoplasmic translational initiation
q=1-347 P formation of cytoplasmic translation initiation complex
q=1-347 P positive regulation of ATPase activity
q=1-347 P translation reinitiation
q=1-347 P translational initiation
r=704-734 C cytoplasmic stress granule
r=704-734 C eukaryotic 43S preinitiation complex
r=704-734 C eukaryotic 48S preinitiation complex
r=704-734 C eukaryotic translation initiation factor 3 complex
r=704-734 C multi-eIF complex
r=704-734 F identical protein binding
r=704-734 F translation initiation factor activity
r=704-734 F translation initiation factor binding
r=704-734 P cytoplasmic translational initiation
r=704-734 P formation of cytoplasmic translation initiation complex
r=704-734 P translational initiation
s=45-96 C cytoplasmic stress granule
s=45-96 C eukaryotic 43S preinitiation complex
s=45-96 C eukaryotic 48S preinitiation complex
s=45-96 C eukaryotic translation initiation factor 3 complex
s=45-96 C multi-eIF complex
s=45-96 F translation initiation factor activity
s=45-96 P formation of cytoplasmic translation initiation complex
s=45-96 P positive regulation of ATPase activity
s=45-96 P translation reinitiation
s=45-96 P translational initiation
s=45-96 P translational termination
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  
3jap.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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