7TM3: UL2
Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate in complex with the multipass translocon. Determined by electron microscopy at 3.25 Å resolution. Released 19 Oct 2022.
- Method
- Electron microscopy
- Resolution
- 3.25 Å
- Organisms
- Oryctolagus cuniculus, Canis lupus
- Chains
- 54
- Atoms
- 149,944
- Mol. weight
- 2356.14 kDa
- Ligands
- ZN, MG
- Released
- 19 Oct 2022
Explore 7TM3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7TM3 contains 394 α-helices and 364 β-strands across 50 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 1: 25 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-4 | 3 | |
| α-helix | 5-15 | 11 | |
| α-helix | 19-22 | 4 | |
| α-helix | 25-27 | 3 | |
| α-helix | 28-47 | 20 | |
| β-strand | 49 | 1 | 100 |
| α-helix | 50 | 1 | |
| α-helix | 63-69 | 7 | |
| β-strand | 75 | 1 | 100 |
| α-helix | 82-97 | 16 | |
| α-helix | 106-133 | 28 | |
| α-helix | 140-143 | 4 | |
| α-helix | 145-168 | 24 | |
| α-helix | 169-173 | 5 | |
| α-helix | 178-196 | 19 | |
| β-strand | 200-202 | 3 | 101 |
| β-strand | 207-209 | 3 | 101 |
| α-helix | 212-222 | 11 | |
| α-helix | 226-234 | 9 | |
| α-helix | 242-259 | 18 | |
| β-strand | 262-269 | 8 | 102 |
| β-strand | 276-282 | 7 | 102 |
| α-helix | 289-311 | 23 | |
| α-helix | 316-321 | 6 | |
| β-strand | 323-327 | 5 | 103 |
| β-strand | 334-339 | 6 | 103 |
| α-helix | 341-345 | 5 | |
| α-helix | 347-348 | 2 | |
| α-helix | 351-356 | 6 | |
| α-helix | 358-383 | 26 | |
| α-helix | 387-396 | 10 | |
| β-strand | 399-401 | 3 | 102 |
| α-helix | 406-438 | 33 | |
| α-helix | 444-464 | 21 | |
Chain 2: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 70-95 | 26 | |
Chain 3: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-24 | 23 | |
| β-strand | 26 | 1 | 102 |
| α-helix | 27-29 | 3 | |
| α-helix | 30-65 | 36 | |
Chain 4: 17 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 137-178 | 42 | |
| β-strand | 181-182 | 2 | 110 |
| β-strand | 198-201 | 4 | 110 |
| β-strand | 204-210 | 7 | 110 |
| β-strand | 212 | 1 | 110 |
| β-strand | 215-223 | 9 | 110 |
| α-helix | 230-238 | 9 | |
| β-strand | 244-251 | 8 | 110 |
| α-helix | 252 | 1 | |
| β-strand | 260-265 | 6 | 110 |
| α-helix | 266-275 | 10 | |
| β-strand | 276 | 1 | 111 |
| α-helix | 277-282 | 6 | |
| α-helix | 286-287 | 2 | |
| β-strand | 288-289 | 2 | 110 |
| α-helix | 290-293 | 4 | |
| β-strand | 299-303 | 5 | 110 |
| α-helix | 306-312 | 7 | |
| α-helix | 315-323 | 9 | |
| α-helix | 325-327 | 3 | |
| β-strand | 328-337 | 10 | 110 |
| β-strand | 340 | 1 | 111 |
| α-helix | 352-354 | 3 | |
| β-strand | 356-364 | 9 | 110 |
| α-helix | 365 | 1 | |
| α-helix | 373-377 | 5 | |
| α-helix | 380-395 | 16 | |
| α-helix | 400-420 | 21 | |
| α-helix | 422-445 | 24 | |
| α-helix | 450-475 | 26 | |
Chain 5: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10 | 1 | 110 |
| α-helix | 20-22 | 3 | |
| α-helix | 32-51 | 20 | |
| α-helix | 54-70 | 17 | |
| α-helix | 77-96 | 20 | |
Chain 6: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-23 | 22 | |
| α-helix | 32-56 | 25 | |
| α-helix | 58-60 | 3 | |
| α-helix | 67-76 | 10 | |
| α-helix | 78-90 | 13 | |
| α-helix | 95-111 | 17 | |
| α-helix | 112-116 | 5 | |
| α-helix | 117-123 | 7 | |
| α-helix | 130-157 | 28 | |
| α-helix | 165-190 | 26 | |
| α-helix | 194-222 | 29 | |
Chain 7: 25 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-8 | 7 | 115 |
| α-helix | 9-10 | 2 | |
| β-strand | 11-14 | 4 | 116 |
| β-strand | 17-20 | 4 | 116 |
| β-strand | 21 | 1 | 117 |
| β-strand | 27-32 | 6 | 115 |
| β-strand | 39 | 1 | 118 |
| β-strand | 41-46 | 6 | 115 |
| α-helix | 52-60 | 9 | |
| β-strand | 63 | 1 | 118 |
| β-strand | 65-70 | 6 | 115 |
| α-helix | 71 | 1 | |
| α-helix | 79-94 | 16 | |
| β-strand | 97 | 1 | 117 |
| β-strand | 101-105 | 5 | 115 |
| α-helix | 108-126 | 19 | |
| α-helix | 129-138 | 10 | |
| α-helix | 140 | 1 | |
| β-strand | 141-146 | 6 | 115 |
| α-helix | 149-151 | 3 | |
| β-strand | 153-154 | 2 | 116 |
| β-strand | 158-166 | 9 | 119 |
| β-strand | 176-182 | 7 | 119 |
| β-strand | 185 | 1 | 120 |
| α-helix | 190-192 | 3 | |
| α-helix | 196-201 | 6 | |
| α-helix | 202-218 | 17 | |
| β-strand | 227-233 | 7 | 119 |
| α-helix | 236-238 | 3 | |
| α-helix | 241-252 | 12 | |
| α-helix | 257-262 | 6 | |
| β-strand | 263-269 | 7 | 119 |
| β-strand | 277-282 | 6 | 119 |
| α-helix | 285-287 | 3 | |
| α-helix | 291-306 | 16 | |
| β-strand | 311-316 | 6 | 119 |
| α-helix | 329-335 | 7 | |
| β-strand | 340-344 | 5 | 119 |
| α-helix | 352-355 | 4 | |
| α-helix | 361-363 | 3 | |
| α-helix | 366-385 | 20 | |
| α-helix | 401-403 | 3 | |
| α-helix | 407-419 | 13 | |
| β-strand | 423 | 1 | 120 |
| α-helix | 432-444 | 13 | |
| β-strand | 446-454 | 9 | 119 |
| β-strand | 462-465 | 4 | 116 |
| β-strand | 469-477 | 9 | 115 |
| α-helix | 480-502 | 23 | |
| α-helix | 504-520 | 17 | |
Chain a: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 42-47 | 6 | |
| β-strand | 72-74 | 3 | 113 |
| α-helix | 84-92 | 9 | |
| β-strand | 98 | 1 | 57 |
| β-strand | 100-102 | 3 | 114 |
| β-strand | 110-112 | 3 | 113 |
| β-strand | 122-126 | 5 | 114 |
| β-strand | 128-129 | 2 | 113 |
| α-helix | 131-138 | 8 | |
| β-strand | 142-146 | 5 | 114 |
42 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) |
| Nascent chain | B | protein | 229 | Oryctolagus cuniculus | |
| uL4 | C | protein | 425 | Oryctolagus cuniculus | G1SVW5 (AlphaFold model) |
| uL18 | D | protein | 297 | Oryctolagus cuniculus | P19949 (AlphaFold model) |
| eL6 | E | protein | 291 | Oryctolagus cuniculus | G1SKF7 (AlphaFold model) |
| uL30 | F | protein | 247 | Oryctolagus cuniculus | G1SV32 |
| eL8 | G | protein | 319 | Oryctolagus cuniculus | G1STW0 |
| uL6 | H | protein | 192 | Oryctolagus cuniculus | G1SWI6 |
| uL16 | I | protein | 214 | Oryctolagus cuniculus | B7NZQ2 |
| uL5 | J | protein | 178 | Oryctolagus cuniculus | G1TUB8 |
| eL13 | L | protein | 211 | Oryctolagus cuniculus | G1TPV0 |
| eL14 | M | protein | 218 | Oryctolagus cuniculus | G1SZ12 |
42 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>7TM3_1 uL2 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 2 (B), FASTA
>7TM3_2 Nascent chain (chains B)
MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVTASAWSHPQFEKGGGSGGGSGGSAWSH
PQFEKAGGSAGSGGGSAGGSALSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLFGSAG
SGGGSAGGGSAAEPWQFSMLAAYMFLLIMLGFPINCLTLYVTVQHKKLRTPLNYILLNLA
VADLFMVFGGFTTTLYTSLHGYFVFGPTGMPGPTPSGTNVGSSGRSPSV
Sequence of entity 3 (C), FASTA
>7TM3_3 uL4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKVKKPRAVGIKQKKKPVVGRKAAAAKKPAADKKAADKRAGPED
KKPAA
Sequence of entity 4 (D), FASTA
>7TM3_4 uL18 (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 5 (E), FASTA
>7TM3_5 eL6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF
Sequence of entity 6 (F), FASTA
>7TM3_6 uL30 (chains F)
MEGAEEKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEY
RQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGT
FVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGK
YNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQIN
RLIRRMN
Sequence of entity 7 (G), FASTA
>7TM3_7 eL8 (chains G)
MSSYRLGYCMKEERHNLVLCLWSQSPGILNSKCLWPFTNIHLLVGALPREGAGGAWGGGR
SEQLPTCSTTHHDFTWDKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQR
AILYKRLKVPPAINQFTQVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGD
VPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGK
ARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSV
ARIAKLEKAKAKELATKLG
Sequence of entity 8 (H), FASTA
>7TM3_8 uL6 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE
Sequence of entity 9 (I), FASTA
>7TM3_9 uL16 (chains I)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS
Sequence of entity 10 (J), FASTA
>7TM3_10 uL5 (chains J)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK
Sequence of entity 11 (L), FASTA
>7TM3_11 eL13 (chains L)
MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK
Sequence of entity 12 (M), FASTA
>7TM3_12 eL14 (chains M)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRN
RIIKNEVKKLQRAALLKASPKKAPVAKGAVAAAAAAAKVPAKKATAAGKKAAAQKAPAQK
APAQKAAGQKAAQPPKAQKGQKPPAQKAPAPKASGKKA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 5 |
| MG | Magnesium ion | Mg | 220 |
Primary citation
Mechanism of an intramembrane chaperone for multipass membrane proteins. Smalinskaite, L., Kim, M.K., Lewis, A.J.O. et al. Nature (2022) 611:161-166. DOI 10.1038/s41586-022-05336-2 · 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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