3JAI: UL2
Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codon. Determined by electron microscopy at 3.65 Å resolution. Released 12 Aug 2015.
- Method
- Electron microscopy
- Resolution
- 3.65 Å
- Organisms
- Oryctolagus cuniculus, Homo sapiens
- Chains
- 87
- Atoms
- 226,453
- Mol. weight
- 3343.93 kDa
- Ligands
- ADP, SF4, ZN, MG
- Released
- 12 Aug 2015
Explore 3JAI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3JAI contains 559 α-helices and 626 β-strands across 79 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain a: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 8-11 | 4 | |
| α-helix | 42-48 | 7 | |
| α-helix | 65-67 | 3 | |
| β-strand | 72-74 | 3 | 202 |
| α-helix | 84-88 | 5 | |
| β-strand | 100-102 | 3 | 203 |
| α-helix | 103-106 | 4 | |
| β-strand | 110-112 | 3 | 202 |
| β-strand | 123-126 | 4 | 203 |
| β-strand | 128-129 | 2 | 202 |
| α-helix | 131-140 | 10 | |
| β-strand | 143-146 | 4 | 203 |
Chain A: 13 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 9-11 | 3 | |
| β-strand | 18 | 1 | 1 |
| α-helix | 19 | 1 | |
| α-helix | 30-32 | 3 | |
| α-helix | 34-38 | 5 | |
| β-strand | 41-48 | 8 | 2 |
| β-strand | 58-62 | 5 | 2 |
| β-strand | 73-77 | 5 | 2 |
| α-helix | 78 | 1 | |
| β-strand | 79 | 1 | 3 |
| β-strand | 83 | 1 | 4 |
| β-strand | 86-90 | 5 | 2 |
| β-strand | 101-103 | 3 | 2 |
| α-helix | 108 | 1 | |
| β-strand | 112-114 | 3 | 2 |
| β-strand | 116 | 1 | 5 |
| β-strand | 126 | 1 | 5 |
| β-strand | 134-140 | 7 | 2 |
| α-helix | 142-144 | 3 | |
| β-strand | 145-149 | 5 | 2 |
| β-strand | 155-159 | 5 | 2 |
| β-strand | 163-166 | 4 | 2 |
| α-helix | 168 | 1 | |
| β-strand | 169 | 1 | 3 |
| α-helix | 174-176 | 3 | |
| α-helix | 182-190 | 9 | |
| β-strand | 193 | 1 | 1 |
| α-helix | 198-200 | 3 | |
| α-helix | 201-203 | 3 | |
| β-strand | 224-225 | 2 | 6 |
| β-strand | 237-238 | 2 | 6 |
Chain aa: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 206 |
| β-strand | 29-31 | 3 | 206 |
| β-strand | 36-40 | 5 | 207 |
| β-strand | 43 | 1 | 208 |
| α-helix | 49-55 | 7 | |
| β-strand | 57 | 1 | 140 |
| β-strand | 66 | 1 | 208 |
| β-strand | 69-73 | 5 | 207 |
| α-helix | 75-80 | 6 | |
| α-helix | 91-93 | 3 | |
| α-helix | 96-98 | 3 | |
Chain AA: 11 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-21 | 10 | |
| β-strand | 25 | 1 | 204 |
| α-helix | 35-37 | 3 | |
| β-strand | 40-41 | 2 | 204 |
| β-strand | 47-48 | 2 | 204 |
| α-helix | 49-50 | 2 | |
| α-helix | 51-67 | 17 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 205 |
| α-helix | 83-94 | 12 | |
| β-strand | 97-100 | 4 | 205 |
| β-strand | 121-123 | 3 | 205 |
| α-helix | 131-136 | 6 | |
| β-strand | 144-148 | 5 | 205 |
| β-strand | 159-162 | 4 | 205 |
| α-helix | 168-184 | 17 | |
| α-helix | 194-195 | 2 | |
| α-helix | 200-202 | 3 | |
| α-helix | 203-206 | 4 | |
Chain b: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-19 | 8 | |
| α-helix | 22-26 | 5 | |
| α-helix | 37-48 | 12 | |
| α-helix | 55-75 | 21 | |
Chain B: 15 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| β-strand | 42-43 | 2 | 15 |
| β-strand | 45-60 | 16 | 16 |
| β-strand | 70-80 | 11 | 16 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-92 | 9 | 17 |
| β-strand | 101-106 | 6 | 17 |
| α-helix | 112-116 | 5 | |
| α-helix | 131-134 | 4 | |
| α-helix | 135-138 | 4 | |
| α-helix | 140-155 | 16 | |
| β-strand | 159-165 | 7 | 17 |
| α-helix | 168-170 | 3 | |
| α-helix | 178-179 | 2 | |
| β-strand | 180-184 | 5 | 17 |
| β-strand | 185-186 | 2 | 15 |
| α-helix | 190-199 | 10 | |
| β-strand | 203-205 | 3 | 17 |
| α-helix | 207-210 | 4 | |
| β-strand | 217-222 | 6 | 16 |
| α-helix | 223-225 | 3 | |
| β-strand | 228-229 | 2 | 18 |
| α-helix | 231-235 | 5 | |
| α-helix | 237-241 | 5 | |
| β-strand | 270-271 | 2 | 18 |
| β-strand | 276-278 | 3 | 16 |
| β-strand | 282 | 1 | 16 |
| β-strand | 284-288 | 5 | 16 |
| β-strand | 293 | 1 | 19 |
| β-strand | 297 | 1 | 19 |
| β-strand | 320 | 1 | 20 |
| β-strand | 324 | 1 | 20 |
| β-strand | 330-334 | 5 | 16 |
| β-strand | 344-349 | 6 | 16 |
| α-helix | 357-360 | 4 | |
| β-strand | 365-368 | 4 | 16 |
| α-helix | 382-389 | 8 | |
Chain bb: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| β-strand | 32-35 | 4 | 12 |
| β-strand | 44-47 | 4 | 12 |
| β-strand | 55 | 1 | 13 |
| β-strand | 62 | 1 | 13 |
| β-strand | 64-65 | 2 | 14 |
| β-strand | 72-73 | 2 | 14 |
Chain BB: 10 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-27 | 3 | |
| β-strand | 30-34 | 5 | 7 |
| β-strand | 46-48 | 3 | 7 |
| α-helix | 50-52 | 3 | |
| β-strand | 53 | 1 | 8 |
| β-strand | 55 | 1 | 8 |
| α-helix | 58-62 | 5 | |
| β-strand | 66 | 1 | 7 |
| β-strand | 69-70 | 2 | 9 |
| α-helix | 71-73 | 3 | |
| β-strand | 82-84 | 3 | 9 |
| β-strand | 87-91 | 5 | 7 |
| β-strand | 95-99 | 5 | 7 |
| β-strand | 104-105 | 2 | 9 |
| α-helix | 109-113 | 5 | |
| β-strand | 120-121 | 2 | 10 |
| β-strand | 124-128 | 5 | 11 |
| β-strand | 134-138 | 5 | 11 |
| β-strand | 141-142 | 2 | 10 |
| α-helix | 143-146 | 4 | |
| α-helix | 158-177 | 20 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-201 | 10 | |
| β-strand | 214-219 | 6 | 11 |
| α-helix | 225-231 | 7 | |
71 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| uL2 | A | protein | 244 | Oryctolagus cuniculus | G1TT27 (AlphaFold model) |
| uL3 | B | protein | 394 | Oryctolagus cuniculus | G1TL06 (AlphaFold model) |
| uL4 | C | protein | 361 | Oryctolagus cuniculus | G1SVW5 (AlphaFold model) |
| uL18 | D | protein | 292 | Oryctolagus cuniculus | P19949 (AlphaFold model) |
| eL6 | E | protein | 248 | Oryctolagus cuniculus | G1TG04 |
| uL30 | F | protein | 225 | Oryctolagus cuniculus | |
| eL8 | G | protein | 241 | Oryctolagus cuniculus | G1STW0 |
| uL6 | H | protein | 190 | Oryctolagus cuniculus | G1SWI6 |
| uL16 | I | protein | 213 | Oryctolagus cuniculus | B7NZQ2 |
| uL5 | J | protein | 169 | Oryctolagus cuniculus | G1TUB8 |
| eL13 | L | protein | 210 | Oryctolagus cuniculus | |
| eL14 | M | protein | 138 | Oryctolagus cuniculus | G1SZ12 |
75 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>3JAI_1 uL2 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGR
Sequence of entity 2 (B), FASTA
>3JAI_2 uL3 (chains B)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD
Sequence of entity 3 (C), FASTA
>3JAI_3 uL4 (chains C)
ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQ
TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKR
YAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIK
KVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLA
PGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAAK
S
Sequence of entity 4 (D), FASTA
>3JAI_4 uL18 (chains D)
FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIIC
QIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQ
VEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPG
YDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKK
AHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA
Sequence of entity 5 (E), FASTA
>3JAI_5 eL6 (chains E)
PHCSRNPVLVRGIGRYSRSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDK
NGGTRVVKLRKMPRYYPTEDVPRKLLSHGRKPFSQHVRKLRASITPGTILIILTGRHRGK
RVVFLKQLSSGLLLVTGPLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKK
QLRKPRHQEGEIFDTEKEKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNG
VYPHKLVF
Sequence of entity 6 (F), FASTA
>3JAI_6 uL30 (chains F)
NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYV
PAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWG
YPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKE
ANNFLWPFKLSSPRGGMKKKTTHFVEGEDAGNREDQINRLIRRMN
Sequence of entity 7 (G), FASTA
>3JAI_7 eL8 (chains G)
KVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQ
VLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTT
LVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGKARLGRLVHRKTCTTVAFT
QVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKL
G
Sequence of entity 8 (H), FASTA
>3JAI_8 uL6 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQA
Sequence of entity 9 (I), FASTA
>3JAI_9 uL16 (chains I)
GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLS
SEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGK
PQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADEF
EDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS
Sequence of entity 10 (J), FASTA
>3JAI_10 uL5 (chains J)
ENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKI
AVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGL
DFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPG
Sequence of entity 11 (L), FASTA
>3JAI_11 eL13 (chains L)
APSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPASGPLRPIVRC
PTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYR
SKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFAS
LRMARANARLFGIRAKRAKEAAEQDVEKKK
Sequence of entity 12 (M), FASTA
>3JAI_12 eL14 (chains M)
VFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDFI
LKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRNR
IIKNEVKKLQRAALLKAS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 2 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
| ZN | Zinc ion | Zn | 8 |
| MG | Magnesium ion | Mg | 195 |
Primary citation
Structural basis for stop codon recognition in eukaryotes. Brown, A., Shao, S., Murray, J. et al. Nature (2015) 524:493-496. DOI 10.1038/nature14896 · PubMed
Other PDB entries of the same protein (UniProt G1TT27 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
- 8SCB 2.5 Å, Terminating ribosome with SRI-41315
- 9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
- 9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
- 8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
- 8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
- 8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
- 8B6C 2.79 Å, Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative…
- 6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
- 7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
- 9BDL 2.8 Å, 80S ribosome with angiogenin
- 9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1
Browse structure collections
About this viewer
MolViewer shows 3JAI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.