8VVP: UL3
Codon sampling state obtained from Anisomycin-treated mammalian ribosomes. Determined by electron microscopy at 2.9 Å resolution. Released 30 Jul 2025.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organisms
- Oryctolagus cuniculus, Bos taurus, Lampyridae
- Chains
- 88
- Atoms
- 222,478
- Mol. weight
- 3559.11 kDa
- Ligands
- MG, ZN, ANM, SPD
- Released
- 30 Jul 2025
Explore 8VVP in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8VVP contains 572 α-helices and 565 β-strands across 78 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, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| α-helix | 29-32 | 4 | |
| α-helix | 34-38 | 5 | |
| β-strand | 41-49 | 9 | 1 |
| α-helix | 50-51 | 2 | |
| α-helix | 57 | 1 | |
| 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 |
| α-helix | 142-144 | 3 | |
| β-strand | 145-149 | 5 | 1 |
| β-strand | 155-159 | 5 | 1 |
| β-strand | 163-166 | 4 | 1 |
| β-strand | 169 | 1 | 2 |
| α-helix | 174-176 | 3 | |
| α-helix | 182-190 | 9 | |
| 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 | 23-25 | 3 | |
| 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 | 175 |
| α-helix | 32-37 | 6 | |
| β-strand | 38-41 | 4 | 175 |
| β-strand | 47-49 | 3 | 175 |
| α-helix | 50 | 1 | |
| α-helix | 51-66 | 16 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 176 |
| α-helix | 84-94 | 11 | |
| β-strand | 97-100 | 4 | 176 |
| β-strand | 121-124 | 4 | 176 |
| α-helix | 131-137 | 7 | |
| β-strand | 144-148 | 5 | 176 |
| β-strand | 159-162 | 4 | 176 |
| 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 | 177 |
| β-strand | 29-31 | 3 | 177 |
| β-strand | 36-43 | 8 | 178 |
| α-helix | 50-56 | 7 | |
| β-strand | 57 | 1 | 124 |
| α-helix | 62-64 | 3 | |
| β-strand | 66-73 | 8 | 178 |
| α-helix | 75-80 | 6 | |
| α-helix | 91-93 | 3 | |
| α-helix | 97-99 | 3 | |
Chain b: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-20 | 15 | |
| α-helix | 37-48 | 12 | |
| β-strand | 52-54 | 3 | 99 |
| α-helix | 58-68 | 11 | |
| α-helix | 73-78 | 6 | |
| β-strand | 88-90 | 3 | 99 |
| α-helix | 95-105 | 11 | |
| α-helix | 108-111 | 4 | |
| α-helix | 135-140 | 6 | |
| β-strand | 145-147 | 3 | 100 |
| β-strand | 152-154 | 3 | 100 |
| α-helix | 227-233 | 7 | |
Chain B: 18 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| α-helix | 14-16 | 3 | |
| α-helix | 40-41 | 2 | |
| β-strand | 42-43 | 2 | 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 | 112-117 | 6 | |
| α-helix | 134-136 | 3 | |
| 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 | 185-186 | 2 | 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 | 158-178 | 21 | |
| 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 | |
70 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 |
|---|
| uL3 | A | protein | 257 | Oryctolagus cuniculus | G1TT27 (AlphaFold model) |
| uL2 | 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 |
| L13 | K | protein | 210 | Oryctolagus cuniculus | G1TPV0 |
| eL14 | L | protein | 218 | Oryctolagus cuniculus | G1SZ12 |
76 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>8VVP_1 uL3 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 2 (B), FASTA
>8VVP_2 uL2 (chains B)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 3 (C), FASTA
>8VVP_3 uL4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKKKPVVGRKAAAAKKPAADKKAADKRAGPEDKKPAA
Sequence of entity 4 (D), FASTA
>8VVP_4 uL18 (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 5 (E), FASTA
>8VVP_5 L6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF
Sequence of entity 6 (F), FASTA
>8VVP_6 uL30 (chains F)
LFANNIREKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHK
EYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFN
GTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSL
GKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQ
INRLIRRMN
Sequence of entity 7 (G), FASTA
>8VVP_7 L7A (chains G)
MSSYRLGYCMKEERHNLVLCLWSQSPGILNSKCLWPFTNIHLLVGALPREGAGGAWGGGR
SEQLPTCSTTHHDFTWDKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQR
AILYKRLKVPPAINQFTQVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGD
VPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGK
ARLCRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSV
ARIAKLEKAKAKELATKLG
Sequence of entity 8 (H), FASTA
>8VVP_8 L9 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE
Sequence of entity 9 (I), FASTA
>8VVP_9 L10 (chains I)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS
Sequence of entity 10 (J), FASTA
>8VVP_10 uL5 (chains J)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK
Sequence of entity 11 (K), FASTA
>8VVP_11 L13 (chains K)
APSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVRC
PTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYR
SKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFAS
LRMARANARLFGIRAKRAKEAAEQDVEKKK
Sequence of entity 12 (L), FASTA
>8VVP_12 eL14 (chains L)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRN
RIIKNEVKKLQRAALLKASPKKAPVAKGAVAAAAAAAKVPAKKATAAGKKAAAQKAPAQK
APAQKAAGQKAAQPPKAQKGQKPPAQKAPAPKASGKKA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 260 |
| ZN | Zinc ion | Zn | 8 |
| ANM | Anisomycin | C14 H19 N O4 | 1 |
| SPD | Spermidine | C7 H19 N3 | 6 |
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 1 |
| SER | Serine | C3 H7 N O3 | 1 |
| SPM | Spermine | C10 H26 N4 | 2 |
| 5GP | Guanosine-5'-monophosphate | C10 H14 N5 O8 P | 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…
- 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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