3JAH: UL2
Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codon. Determined by electron microscopy at 3.45 Å resolution. Released 12 Aug 2015.
- Method
- Electron microscopy
- Resolution
- 3.45 Å
- Organisms
- Oryctolagus cuniculus, Homo sapiens
- Chains
- 87
- Atoms
- 226,454
- Mol. weight
- 3344.06 kDa
- Ligands
- MG, ZN, SF4, ADP
- Released
- 12 Aug 2015
Explore 3JAH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3JAH contains 534 α-helices and 608 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: 10 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 7-11 | 5 | |
| α-helix | 42-48 | 7 | |
| α-helix | 65-68 | 4 | |
| β-strand | 72-74 | 3 | 194 |
| α-helix | 75-77 | 3 | |
| α-helix | 79-81 | 3 | |
| α-helix | 84-88 | 5 | |
| β-strand | 100-102 | 3 | 195 |
| α-helix | 103-106 | 4 | |
| β-strand | 110-112 | 3 | 194 |
| α-helix | 116-118 | 3 | |
| β-strand | 123-126 | 4 | 195 |
| β-strand | 128-129 | 2 | 194 |
| α-helix | 131-140 | 10 | |
| β-strand | 143-146 | 4 | 195 |
Chain A: 10 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 9-12 | 4 | |
| α-helix | 14-16 | 3 | |
| β-strand | 18 | 1 | 1 |
| α-helix | 19 | 1 | |
| α-helix | 29-32 | 4 | |
| α-helix | 34-38 | 5 | |
| β-strand | 41-49 | 9 | 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 | 87-90 | 4 | 2 |
| β-strand | 101-103 | 3 | 2 |
| β-strand | 112-114 | 3 | 2 |
| β-strand | 116 | 1 | 5 |
| β-strand | 126 | 1 | 5 |
| β-strand | 134-140 | 7 | 2 |
| 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 |
| β-strand | 224-225 | 2 | 6 |
| β-strand | 237-238 | 2 | 6 |
Chain aa: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 199 |
| β-strand | 29-31 | 3 | 199 |
| β-strand | 36 | 1 | 200 |
| β-strand | 39-43 | 5 | 201 |
| α-helix | 46-55 | 10 | |
| β-strand | 66-70 | 5 | 201 |
| β-strand | 73 | 1 | 200 |
| α-helix | 75-80 | 6 | |
| α-helix | 91-93 | 3 | |
| α-helix | 97-98 | 2 | |
Chain AA: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-21 | 10 | |
| β-strand | 25 | 1 | 196 |
| α-helix | 34-37 | 4 | |
| β-strand | 41 | 1 | 197 |
| β-strand | 47 | 1 | 197 |
| β-strand | 48 | 1 | 196 |
| α-helix | 51-67 | 17 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 198 |
| α-helix | 83-94 | 12 | |
| β-strand | 97-100 | 4 | 198 |
| α-helix | 103-104 | 2 | |
| β-strand | 121-124 | 4 | 198 |
| α-helix | 131-136 | 6 | |
| β-strand | 144-148 | 5 | 198 |
| β-strand | 159-162 | 4 | 198 |
| α-helix | 168-184 | 17 | |
| α-helix | 199-202 | 4 | |
Chain b: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-18 | 7 | |
| α-helix | 22-24 | 3 | |
| α-helix | 37-48 | 12 | |
| α-helix | 55-75 | 21 | |
Chain B: 14 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| α-helix | 27-28 | 2 | |
| β-strand | 42-43 | 2 | 13 |
| β-strand | 45-59 | 15 | 14 |
| β-strand | 63 | 1 | 15 |
| β-strand | 65 | 1 | 15 |
| β-strand | 71-80 | 10 | 14 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-94 | 11 | 16 |
| β-strand | 99-106 | 8 | 16 |
| α-helix | 112-117 | 6 | |
| α-helix | 134-138 | 5 | |
| α-helix | 140-156 | 17 | |
| β-strand | 160-165 | 6 | 16 |
| α-helix | 168-170 | 3 | |
| α-helix | 178-179 | 2 | |
| β-strand | 180-184 | 5 | 16 |
| β-strand | 185-186 | 2 | 13 |
| α-helix | 190-199 | 10 | |
| β-strand | 204-205 | 2 | 16 |
| α-helix | 207-210 | 4 | |
| β-strand | 216-222 | 7 | 14 |
| β-strand | 228-229 | 2 | 17 |
| α-helix | 231-234 | 4 | |
| α-helix | 237-240 | 4 | |
| β-strand | 270-271 | 2 | 17 |
| β-strand | 276-288 | 13 | 14 |
| β-strand | 293 | 1 | 18 |
| β-strand | 297 | 1 | 18 |
| β-strand | 320 | 1 | 19 |
| β-strand | 324 | 1 | 19 |
| β-strand | 330-334 | 5 | 14 |
| β-strand | 344-349 | 6 | 14 |
| α-helix | 358-360 | 3 | |
| β-strand | 365-367 | 3 | 14 |
| α-helix | 382-389 | 8 | |
Chain bb: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| β-strand | 32-33 | 2 | 10 |
| β-strand | 34-35 | 2 | 11 |
| β-strand | 46-47 | 2 | 10 |
| β-strand | 54-55 | 2 | 12 |
| β-strand | 62-65 | 4 | 12 |
| β-strand | 72-73 | 2 | 12 |
| β-strand | 79-80 | 2 | 11 |
Chain BB: 10 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-27 | 3 | |
| β-strand | 28-34 | 7 | 7 |
| α-helix | 35-36 | 2 | |
| β-strand | 45-50 | 6 | 7 |
| α-helix | 51-52 | 2 | |
| 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 | 83-84 | 2 | 9 |
| β-strand | 87-91 | 5 | 7 |
| β-strand | 95-99 | 5 | 7 |
| β-strand | 102-104 | 3 | 9 |
| α-helix | 106-113 | 8 | |
| β-strand | 120-128 | 9 | 9 |
| β-strand | 134-142 | 9 | 9 |
| α-helix | 158-177 | 20 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-201 | 10 | |
| β-strand | 211-219 | 9 | 9 |
| α-helix | 225-232 | 8 | |
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 | 362 | 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
>3JAH_1 uL2 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGR
Sequence of entity 2 (B), FASTA
>3JAH_2 uL3 (chains B)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD
Sequence of entity 3 (C), FASTA
>3JAH_3 uL4 (chains C)
ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQ
TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKR
YAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIK
KVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLA
PGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAAK
KS
Sequence of entity 4 (D), FASTA
>3JAH_4 uL18 (chains D)
FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIIC
QIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQ
VEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPG
YDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKK
AHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA
Sequence of entity 5 (E), FASTA
>3JAH_5 eL6 (chains E)
PHCSRNPVLVRGIGRYSRSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDK
NGGTRVVKLRKMPRYYPTEDVPRKLLSHGRKPFSQHVRKLRASITPGTILIILTGRHRGK
RVVFLKQLSSGLLLVTGPLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKK
QLRKPRHQEGEIFDTEKEKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNG
VYPHKLVF
Sequence of entity 6 (F), FASTA
>3JAH_6 uL30 (chains F)
NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYV
PAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWG
YPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKE
ANNFLWPFKLSSPRGGMKKKTTHFVEGEDAGNREDQINRLIRRMN
Sequence of entity 7 (G), FASTA
>3JAH_7 eL8 (chains G)
KVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQ
VLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTT
LVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGKARLGRLVHRKTCTTVAFT
QVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKL
G
Sequence of entity 8 (H), FASTA
>3JAH_8 uL6 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQA
Sequence of entity 9 (I), FASTA
>3JAH_9 uL16 (chains I)
GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLS
SEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGK
PQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADEF
EDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS
Sequence of entity 10 (J), FASTA
>3JAH_10 uL5 (chains J)
ENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKI
AVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGL
DFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPG
Sequence of entity 11 (L), FASTA
>3JAH_11 eL13 (chains L)
APSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPASGPLRPIVRC
PTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYR
SKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFAS
LRMARANARLFGIRAKRAKEAAEQDVEKKK
Sequence of entity 12 (M), FASTA
>3JAH_12 eL14 (chains M)
VFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDFI
LKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRNR
IIKNEVKKLQRAALLKAS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 195 |
| ZN | Zinc ion | Zn | 8 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 2 |
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
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