7OBQ: SRP-SR at the distal site conformation
SRP-SR at the distal site conformation. Determined by electron microscopy at 3.9 Å resolution. Released 21 Jul 2021.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organisms
- Canis lupus familiaris, Saccharomyces cerevisiae, Oryctolagus cuniculus
- Chains
- 8
- Atoms
- 16,668
- Mol. weight
- 400.88 kDa
- Ligands
- MG, GTP, GNP
- Released
- 21 Jul 2021
Explore 7OBQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7OBQ contains 73 α-helices and 40 β-strands across 7 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 q: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-18 | 3 | 1 |
| α-helix | 20-23 | 4 | |
| β-strand | 24 | 1 | 2 |
| β-strand | 41 | 1 | 2 |
| α-helix | 46-54 | 9 | |
| β-strand | 61-67 | 7 | 1 |
| β-strand | 79-84 | 6 | 1 |
| β-strand | 87 | 1 | 3 |
| β-strand | 93 | 1 | 3 |
| α-helix | 101-116 | 16 | |
Chain s: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-19 | 18 | |
Chain u: 18 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 55 | 1 | 4 |
| α-helix | 59-67 | 9 | |
| α-helix | 78-95 | 18 | |
| α-helix | 114-117 | 4 | |
| α-helix | 120-141 | 22 | |
| α-helix | 147-169 | 23 | |
| β-strand | 175 | 1 | 4 |
| α-helix | 177-197 | 21 | |
| α-helix | 201-221 | 21 | |
| α-helix | 224-248 | 25 | |
| α-helix | 253-266 | 14 | |
| α-helix | 269-285 | 17 | |
| α-helix | 286-290 | 5 | |
| α-helix | 305-319 | 15 | |
| α-helix | 331-361 | 31 | |
| α-helix | 374-398 | 25 | |
| α-helix | 416-442 | 27 | |
| α-helix | 447-467 | 21 | |
| α-helix | 479-493 | 15 | |
| α-helix | 512-522 | 11 | |
Chain v: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 66-70 | 5 | 5 |
| α-helix | 77-86 | 10 | |
| β-strand | 92 | 1 | 6 |
| β-strand | 99-104 | 6 | 5 |
| β-strand | 112-117 | 6 | 5 |
| α-helix | 125-131 | 7 | |
| β-strand | 136-144 | 9 | 5 |
| α-helix | 152-167 | 16 | |
| α-helix | 172-173 | 2 | |
| β-strand | 174-180 | 7 | 5 |
| α-helix | 187-189 | 3 | |
| α-helix | 190-207 | 18 | |
| β-strand | 241-245 | 5 | 5 |
| α-helix | 252-256 | 5 | |
| α-helix | 261-270 | 10 | |
Chain x: 19 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 22-41 | 20 | |
| α-helix | 46-63 | 18 | |
| α-helix | 73-87 | 15 | |
| α-helix | 91-94 | 4 | |
| β-strand | 102-108 | 7 | 7 |
| α-helix | 114-127 | 14 | |
| β-strand | 132-136 | 5 | 7 |
| α-helix | 145-155 | 11 | |
| β-strand | 159-160 | 2 | 7 |
| α-helix | 168-181 | 14 | |
| β-strand | 186-190 | 5 | 7 |
| α-helix | 199-212 | 14 | |
| β-strand | 216-222 | 7 | 7 |
| β-strand | 225 | 1 | 8 |
| α-helix | 229-239 | 11 | |
| β-strand | 245-248 | 4 | 7 |
| α-helix | 259-266 | 8 | |
| β-strand | 270-273 | 4 | 7 |
| β-strand | 283-284 | 2 | 7 |
| α-helix | 287-295 | 9 | |
| α-helix | 317-324 | 8 | |
| α-helix | 329-342 | 14 | |
| α-helix | 345-349 | 5 | |
| α-helix | 365-381 | 17 | |
| α-helix | 384-387 | 4 | |
| α-helix | 392-398 | 7 | |
| α-helix | 400-409 | 10 | |
| α-helix | 416-436 | 21 | |
Chain y: 21 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 9 |
| β-strand | 13 | 1 | 6 |
| β-strand | 14-17 | 4 | 9 |
| α-helix | 28-37 | 10 | |
| β-strand | 47-48 | 2 | 9 |
| β-strand | 52-59 | 8 | 9 |
| β-strand | 64-71 | 8 | 9 |
| α-helix | 78-93 | 16 | |
| α-helix | 95-98 | 4 | |
| α-helix | 104-108 | 5 | |
| α-helix | 114-129 | 16 | |
| α-helix | 134-146 | 13 | |
| α-helix | 331-333 | 3 | |
| α-helix | 334-350 | 17 | |
| α-helix | 355-368 | 14 | |
| α-helix | 380-396 | 17 | |
| α-helix | 404-413 | 10 | |
| α-helix | 417 | 1 | |
| β-strand | 418-423 | 6 | 10 |
| α-helix | 430-444 | 15 | |
| β-strand | 448-453 | 6 | 10 |
| α-helix | 460-474 | 15 | |
| β-strand | 486-489 | 4 | 10 |
| α-helix | 497-511 | 15 | |
| β-strand | 515-520 | 6 | 10 |
| α-helix | 528-541 | 14 | |
| β-strand | 545-551 | 7 | 10 |
| β-strand | 554 | 1 | 8 |
| α-helix | 558-571 | 14 | |
| β-strand | 583-587 | 5 | 10 |
| α-helix | 589-591 | 3 | |
| α-helix | 597-605 | 9 | |
| α-helix | 608-609 | 2 | |
| β-strand | 610-614 | 5 | 10 |
| β-strand | 622-623 | 2 | 10 |
| α-helix | 627-635 | 9 | |
Chain z: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 562-566 | 5 | |
| α-helix | 580-582 | 3 | |
| α-helix | 594-599 | 6 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Srp RNA | 1 | RNA | 249 | Canis lupus familiaris | |
| Signal recognition particle 19 | q | protein | 144 | Canis lupus familiaris | J9PAS6 (AlphaFold model) |
| EM14S01-3B_G0054400.mRNA.1.CDS.1 | s | protein | 62 | Saccharomyces cerevisiae | A0A7I9EWR8 |
| Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68 | u | protein | 622 | Canis lupus familiaris | Q00004 (AlphaFold model) |
| Signal recognition particle receptor subunit beta | v | protein | 271 | Oryctolagus cuniculus | G1STG2 (AlphaFold model) |
| Signal recognition particle 54 kDa protein | x | protein | 504 | Canis lupus familiaris | P61010 |
| SRP receptor subunit alpha | y | protein | 637 | Oryctolagus cuniculus | A0A5F9CI80 |
| Signal recognition particle subunit SRP72 | z | protein | 671 | Canis lupus familiaris | P33731 |
Sequence of entity 1 (1), FASTA
>7OBQ_1 SRP RNA (chains 1)
GCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUGAGGCAGGAGGAU
CGCUUCGCUAUGCCGAUCGGGUGUCCGCACUAAGUUCGGCAUCAAUAUGGUGACCUCCCG
GGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAG
CAGGUCAAAACUCCCGUGCUGAUCAGUAGUGGGAUCGCGCCUGUGAAUAGCAUAGCGAGA
CCCCGUCUC
Sequence of entity 2 (q), FASTA
>7OBQ_2 Signal recognition particle 19 (chains q)
MACAAARSPAEQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNV
FLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ
KTGGGDQSLQQGEGSKKGKGKKKK
Sequence of entity 3 (s), FASTA
>7OBQ_3 EM14S01-3B_G0054400.mRNA.1.CDS.1 (chains s)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XX
Sequence of entity 4 (u), FASTA
>7OBQ_4 Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68 (chains u)
MAAEKQVPGGGGGGGGGGGGGGGSGGGRGAGGEENKENERPSAGSKANREFGDSLSLEIL
QIIKESQQQHGLRHGDFQRYRGYCSRRQRRLRKTLNFKMGNRHKFTGKKVTEDLLTDNRY
LLLVLMDAERAWSYAMQLKQEANTEPRKRFHLLSRLRKAVKHAEELERLCESNRVDAKTK
LEAQAYTAYLSGMLRFEHQEWKAAIEAFNKCKTIYEKLASAFTEEQAVLYNQRVEEISPN
IRYCAYNIGDQSAINELMQMRLRSGGTEGLLAEKLEALITQTRAKQAATMSEVEWRGRTV
PVKIDKVRIFLLGLADNEAAIAQAESEETKERLFESMLSECRDAIQAVREELKPDQKQRD
YTLDGESGKVSNLQYLHSYLTYIKLSTAIRRNENMAKGLQKALQQQPEDESKRSPRPQDL
IRLYDIILQNLVELLQLPGLEEDRAFQKEIGLKTLVFKAYRCFFIAQSYVLVKKWSEALV
LYDRVLKYANEVNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 5 (v), FASTA
>7OBQ_5 Signal recognition particle receptor subunit beta (chains v)
MASADSRRLGDGDGAGGAFQPYLDSLRQELQQRDPTVLSVVVALLAVLLTLVFWKLVRSR
RSSQRAVLLLGLCDSGKTLLFVRLLTGHYRDTQTSITDSSATYRVNNNRGNSLTLIDLPG
HESLRLQFLERFKTSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMSLKNTPSFLIACN
KQDIAMAKSAKLIQQQLEKELNTLRVTRSAAPSTLDSSSTAPAQLGKKGKEFEFSQLPLK
VEFLECSAKGGRGDPGSADIQDLEKWLAKIA
Sequence of entity 6 (x), FASTA
>7OBQ_6 Signal recognition particle 54 kDa protein (chains x)
MVLADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAI
DLEEMASGLNKRKMIQHAVFKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGSGKTTTCSK
LAYYYQRKGWKTCLICADTFRAGAFDQLKQNATKARIPFYGSYTEMDPVIIASEGVEKFK
NENFEIIIVDTSGRHKQEDSLFEEMLQVANAIQPDNIVYVMDASIGQACEAQAKAFKDKV
DVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHIDDFEPFKTQPFISKLLGMGDI
EGLIDKVNELKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFM
SKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQEL
LTQYTKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGL
QSMMRQFQQGAAGNMKGMMGFNNM
Sequence of entity 7 (y), FASTA
>7OBQ_7 SRP receptor subunit alpha (chains y)
MLDFFTIFSKGGLVLWCFQGVSDSCTGPVNALIRSVLLQERGGNNSFTHEALTLKYKLDN
QFELVFVVGFQKILTLTYVDKLIDDVHRLFRDKYRTEIQQQSALSLLNGTFDFQNDFLRL
LREAEESSKIRAPTTMKKFEDSEKAKKPVRSMIETRGEKPKEKAKNSKKKGAKKEGSDGP
LATSKAVPAEKSGLPVGPENGVELSKEELIRRKREEFIQKHGRGLEKSSKSKSEAPKEKG
KKAPRVWELGGCANKEVLDYSTPTTNGAPEAALSEDINLIRGTGPGGQLQDLDCSSSDDE
GAAQNSTKPSSTKGTLGGMFGMLKGLVGSKSLSREDMESVLDKMRDHLIAKNVAADIAVQ
LCESVANKLEGKVMGTFSTVTSTVKQALQESLVQILQPQRRVDMLRDIMDAQRRQRPYVV
TFCGVNGVGKSTNLAKISFWLLENGFSVLIAACDTFRAGAVEQLRTHTRRLSALHPPEKH
GGRTMVQLFEKGYGKDAAGIAMEAIAFARNQGFDVVLVDTAGRMQDNAPLMTALAKLITV
NTPDLVLFVGEALVGNEAVDQLVKFNRALADHSMAQTPRLIDGIVLTKFDTIDDKVGAAI
SMTYITSKPIVFVGTGQTYCDLRSLNAKAVVAALMKA
Sequence of entity 8 (z), FASTA
>7OBQ_8 Signal recognition particle subunit SRP72 (chains z)
MASGGSGGVSVPALWSEVNRYGQNGDFTRALKTVNKILQINKDDVTALHCKVVCLIQNGS
FKEALNVINTHTKVLANNSLSFEKAYCEYRLNRIENALKTIESANQQTDKLKELYGQVLY
RLERYDECLAVYRDLVRNSQDDYDEERKTNLSAVVAAQSNWEKVVPENLGLQEGTHELCY
NAACALIGQGQLSQAMKILQKAEDLCRRSLSEDSDGTEEDPQAELAIIHGQMAYILQLQG
RTEEALQLYNQIIKLKPTDVGLLAVIANNIITINKDQNVFDSKKKVKLTNAEGVEFKLSK
KQLQAIEFNKALLAMYTNQAEQCRKISASLQSQSPEHLLPVLIQAAQLCREKQHTKAIEL
LQEFSDQHPENAAEIKLTMAQLKISQGNISKACLILRSIEELKHKPGMVSALVTMYSHEE
DIDSAIEVFTQAIQWYQNHQPKSSAHLSLIREAANFKLKYGRKKEAISDLEQLWKQNPKD
IHTLAQLISAYSLVDPEKAKALSKHLPSSDSMSLKVDVEALENSPGATYIRKKGGKVAGD
SQPKEQGQGDLKKKKKKKKGKLPKNYDPKVTPDPERWLPMRERSYYRGRKKGKKKDQIGK
GTQGATAGASSELDASKTVSSPPTSPRPGSAATASASTSNIIPPRHQKPAGAPATKKKQQ
QKKKKGGKGGW
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 3 |
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 1 |
| GNP | Phosphoaminophosphonic acid-guanylate ester | C10 H17 N6 O13 P3 | 2 |
Primary citation
Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle. Jomaa, A., Eitzinger, S., Zhu, Z. et al. Cell Rep (2021) 36:109350-109350. DOI 10.1016/j.celrep.2021.109350 · PubMed
Other PDB entries of the same protein (UniProt J9PAS6 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7OBR 2.8 Å, RNC-SRP early complex
- 6FRK 3.7 Å, Structure of a prehandover mammalian ribosomal SRP and SRP receptor targeting complex
- 6R6G 3.7 Å, Structure of XBP1u-paused ribosome nascent chain complex with SRP.
- 4UE5 9.0 Å, Structural basis for targeting and elongation arrest of Bacillus signal recognition…
Browse structure collections
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