8VVQ: UL2
Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from merged datasets. Determined by electron microscopy at 2.7 Å resolution. Released 30 Jul 2025.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organisms
- Oryctolagus cuniculus, Bos taurus, Lampyridae
- Chains
- 88
- Atoms
- 222,430
- Mol. weight
- 3560.76 kDa
- Ligands
- MG, ZN, 5GP, ANM
- Released
- 30 Jul 2025
Explore 8VVQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8VVQ contains 575 α-helices and 569 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: 11 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-9 | 4 | |
| α-helix | 10-12 | 3 | |
| α-helix | 29-32 | 4 | |
| α-helix | 34-38 | 5 | |
| β-strand | 41-49 | 9 | 1 |
| α-helix | 50-51 | 2 | |
| β-strand | 58-64 | 7 | 1 |
| β-strand | 71-77 | 7 | 1 |
| β-strand | 79 | 1 | 2 |
| β-strand | 83 | 1 | 3 |
| β-strand | 87-90 | 4 | 1 |
| β-strand | 101-103 | 3 | 1 |
| α-helix | 108 | 1 | |
| β-strand | 112-114 | 3 | 1 |
| β-strand | 116 | 1 | 4 |
| β-strand | 126 | 1 | 4 |
| β-strand | 134-140 | 7 | 1 |
| β-strand | 145-149 | 5 | 1 |
| β-strand | 155-159 | 5 | 1 |
| β-strand | 163-166 | 4 | 1 |
| α-helix | 168 | 1 | |
| β-strand | 169 | 1 | 2 |
| α-helix | 174-176 | 3 | |
| α-helix | 182-190 | 9 | |
| α-helix | 198-200 | 3 | |
| α-helix | 201-203 | 3 | |
| β-strand | 224-225 | 2 | 5 |
| β-strand | 237-238 | 2 | 5 |
Chain AA: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-18 | 7 | |
| α-helix | 22-25 | 4 | |
| α-helix | 37-48 | 12 | |
| α-helix | 49-53 | 5 | |
| α-helix | 54-75 | 22 | |
| α-helix | 91-100 | 10 | |
| α-helix | 106-118 | 13 | |
Chain AB: 11 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-21 | 10 | |
| β-strand | 25 | 1 | 176 |
| α-helix | 32-37 | 6 | |
| β-strand | 38-41 | 4 | 176 |
| β-strand | 47-49 | 3 | 176 |
| α-helix | 50 | 1 | |
| α-helix | 51-66 | 16 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 177 |
| α-helix | 84-94 | 11 | |
| β-strand | 97-100 | 4 | 177 |
| β-strand | 121-124 | 4 | 177 |
| α-helix | 131-137 | 7 | |
| β-strand | 144-148 | 5 | 177 |
| β-strand | 159-162 | 4 | 177 |
| α-helix | 168-186 | 19 | |
| α-helix | 194-195 | 2 | |
| α-helix | 199-202 | 4 | |
| α-helix | 207-217 | 11 | |
Chain AC: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 178 |
| β-strand | 29-31 | 3 | 178 |
| β-strand | 36-43 | 8 | 179 |
| α-helix | 50-56 | 7 | |
| β-strand | 57 | 1 | 125 |
| α-helix | 62-65 | 4 | |
| β-strand | 66-73 | 8 | 179 |
| α-helix | 75-80 | 6 | |
| α-helix | 91-93 | 3 | |
| α-helix | 97-99 | 3 | |
Chain b: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-20 | 15 | |
| α-helix | 37-48 | 12 | |
| β-strand | 52-54 | 3 | 98 |
| α-helix | 58-69 | 12 | |
| α-helix | 73-78 | 6 | |
| β-strand | 88-90 | 3 | 98 |
| α-helix | 95-105 | 11 | |
| α-helix | 108-111 | 4 | |
| β-strand | 125 | 1 | 99 |
| α-helix | 135-139 | 5 | |
| β-strand | 145-147 | 3 | 100 |
| β-strand | 152-154 | 3 | 100 |
| β-strand | 218 | 1 | 99 |
| α-helix | 227-233 | 7 | |
Chain B: 19 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| α-helix | 14-16 | 3 | |
| α-helix | 32-35 | 4 | |
| α-helix | 40-41 | 2 | |
| β-strand | 42 | 1 | 12 |
| β-strand | 45-60 | 16 | 13 |
| β-strand | 70-80 | 11 | 13 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-95 | 12 | 14 |
| β-strand | 98-106 | 9 | 14 |
| α-helix | 112-115 | 4 | |
| α-helix | 133-136 | 4 | |
| α-helix | 140-156 | 17 | |
| β-strand | 159-165 | 7 | 14 |
| α-helix | 168-170 | 3 | |
| α-helix | 178-179 | 2 | |
| β-strand | 180-184 | 5 | 14 |
| β-strand | 186 | 1 | 12 |
| α-helix | 190-200 | 11 | |
| β-strand | 204-205 | 2 | 14 |
| α-helix | 207-209 | 3 | |
| β-strand | 216-222 | 7 | 13 |
| α-helix | 223-225 | 3 | |
| β-strand | 228-229 | 2 | 15 |
| α-helix | 231-234 | 4 | |
| α-helix | 237-241 | 5 | |
| β-strand | 270-271 | 2 | 15 |
| β-strand | 276-287 | 12 | 13 |
| β-strand | 292-294 | 3 | 16 |
| β-strand | 297-299 | 3 | 16 |
| α-helix | 316 | 1 | |
| β-strand | 320 | 1 | 17 |
| β-strand | 324 | 1 | 17 |
| β-strand | 330-334 | 5 | 13 |
| β-strand | 344-349 | 6 | 13 |
| α-helix | 357-360 | 4 | |
| β-strand | 365-368 | 4 | 13 |
| α-helix | 382-389 | 8 | |
| α-helix | 393-396 | 4 | |
Chain BA: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-24 | 12 | |
| β-strand | 26-29 | 4 | 18 |
| α-helix | 31-40 | 10 | |
| β-strand | 45-48 | 4 | 18 |
| α-helix | 54-67 | 14 | |
| β-strand | 70-73 | 4 | 18 |
| α-helix | 78-85 | 8 | |
| β-strand | 93-98 | 6 | 18 |
| α-helix | 104-107 | 4 | |
Chain BB: 9 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-27 | 4 | |
| β-strand | 28-34 | 7 | 6 |
| β-strand | 43-50 | 8 | 6 |
| α-helix | 51-52 | 2 | |
| β-strand | 53 | 1 | 7 |
| β-strand | 56 | 1 | 7 |
| α-helix | 58-62 | 5 | |
| β-strand | 66-70 | 5 | 6 |
| α-helix | 71-73 | 3 | |
| β-strand | 82-91 | 10 | 6 |
| β-strand | 95-105 | 11 | 6 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-128 | 9 | 6 |
| β-strand | 134-142 | 9 | 6 |
| β-strand | 143 | 1 | 8 |
| α-helix | 158-177 | 20 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-201 | 10 | |
| β-strand | 207 | 1 | 8 |
| β-strand | 211-219 | 9 | 6 |
| 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 | 257 | Oryctolagus cuniculus | G1TT27 (AlphaFold model) |
| uL3 | B | protein | 403 | Oryctolagus cuniculus | G1TL06 (AlphaFold model) |
| uL4 | C | protein | 413 | Oryctolagus cuniculus | G1SVW5 (AlphaFold model) |
| uL18 | D | protein | 297 | Oryctolagus cuniculus | P19949 (AlphaFold model) |
| L6 | E | protein | 291 | Oryctolagus cuniculus | G1SKF7 |
| uL30 | F | protein | 249 | Oryctolagus cuniculus | G1SV32 |
| L7A | G | protein | 319 | Oryctolagus cuniculus | G1STW0 |
| L9 | H | protein | 192 | Oryctolagus cuniculus | G1SWI6 |
| L10 | I | protein | 214 | Oryctolagus cuniculus | B7NZQ2 |
| uL5 | J | protein | 178 | Oryctolagus cuniculus | G1TUB8 |
| eL13 | K | protein | 211 | Oryctolagus cuniculus | G1TPV0 |
| eL14 | L | protein | 218 | Oryctolagus cuniculus | G1SZ12 |
76 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>8VVQ_1 uL2 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 2 (B), FASTA
>8VVQ_2 uL3 (chains B)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 3 (C), FASTA
>8VVQ_3 uL4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKKKPVVGRKAAAAKKPAADKKAADKRAGPEDKKPAA
Sequence of entity 4 (D), FASTA
>8VVQ_4 uL18 (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 5 (E), FASTA
>8VVQ_5 L6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF
Sequence of entity 6 (F), FASTA
>8VVQ_6 uL30 (chains F)
LFANNIREKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHK
EYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFN
GTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSL
GKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQ
INRLIRRMN
Sequence of entity 7 (G), FASTA
>8VVQ_7 L7A (chains G)
MSSYRLGYCMKEERHNLVLCLWSQSPGILNSKCLWPFTNIHLLVGALPREGAGGAWGGGR
SEQLPTCSTTHHDFTWDKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQR
AILYKRLKVPPAINQFTQVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGD
VPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGK
ARLCRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSV
ARIAKLEKAKAKELATKLG
Sequence of entity 8 (H), FASTA
>8VVQ_8 L9 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE
Sequence of entity 9 (I), FASTA
>8VVQ_9 L10 (chains I)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS
Sequence of entity 10 (J), FASTA
>8VVQ_10 uL5 (chains J)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK
Sequence of entity 11 (K), FASTA
>8VVQ_11 eL13 (chains K)
MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK
Sequence of entity 12 (L), FASTA
>8VVQ_12 eL14 (chains L)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRN
RIIKNEVKKLQRAALLKASPKKAPVAKGAVAAAAAAAKVPAKKATAAGKKAAAQKAPAQK
APAQKAAGQKAAQPPKAQKGQKPPAQKAPAPKASGKKA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 290 |
| ZN | Zinc ion | Zn | 8 |
| 5GP | Guanosine-5'-monophosphate | C10 H14 N5 O8 P | 1 |
| ANM | Anisomycin | C14 H19 N O4 | 1 |
| SPD | Spermidine | C7 H19 N3 | 1 |
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 1 |
| SER | Serine | C3 H7 N O3 | 1 |
Water and common crystallization additives (K) are not listed.
Primary citation
Rapid purification reveals structural insights into transient ribosome states. Loerch, S., Petrossian, E., Smith, P.R. et al. To be published.
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…
- 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
- 9NDP 2.82 Å, Structure of stalled ribosome and nascent chain in complex with NMT2 and NAC
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