6Y32: GTPase heterodimer of human SRP54 and SRalpha
Structure of the GTPase heterodimer of human SRP54 and SRalpha. Determined by X-ray diffraction at 2.6 Å resolution. Released 23 Sept 2020.
- Method
- X-ray diffraction
- Resolution
- 2.6 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 18,356
- Mol. weight
- 277.7 kDa
- Ligands
- GNP, MG
- Released
- 23 Sept 2020
Explore 6Y32 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6Y32 contains 98 α-helices and 72 β-strands across 8 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, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-41 | 19 | |
| α-helix | 46-58 | 13 | |
| α-helix | 71-87 | 17 | |
| α-helix | 92-94 | 3 | |
| β-strand | 102-108 | 7 | 1 |
| α-helix | 114-127 | 14 | |
| β-strand | 132-136 | 5 | 1 |
| α-helix | 144-154 | 11 | |
| β-strand | 159-160 | 2 | 1 |
| α-helix | 168-181 | 14 | |
| β-strand | 186-190 | 5 | 1 |
| α-helix | 199-212 | 14 | |
| β-strand | 216-222 | 7 | 1 |
| β-strand | 225 | 1 | 2 |
| α-helix | 229-239 | 11 | |
| β-strand | 244-248 | 5 | 1 |
| α-helix | 258-266 | 9 | |
| β-strand | 270-274 | 5 | 1 |
| β-strand | 282-284 | 3 | 1 |
| α-helix | 287-295 | 9 | |
Chain B: 12 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 332-351 | 20 | |
| α-helix | 356-370 | 15 | |
| α-helix | 378-397 | 20 | |
| α-helix | 405-415 | 11 | |
| β-strand | 419-424 | 6 | 3 |
| α-helix | 431-444 | 14 | |
| β-strand | 449-454 | 6 | 3 |
| α-helix | 461-472 | 12 | |
| α-helix | 473-475 | 3 | |
| β-strand | 487-490 | 4 | 3 |
| α-helix | 498-512 | 15 | |
| β-strand | 516-521 | 6 | 3 |
| α-helix | 529-542 | 14 | |
| β-strand | 546-552 | 7 | 3 |
| β-strand | 555 | 1 | 2 |
| α-helix | 558-572 | 15 | |
| β-strand | 584-588 | 5 | 3 |
| α-helix | 599-606 | 8 | |
| β-strand | 611-615 | 5 | 3 |
| β-strand | 623-624 | 2 | 3 |
| α-helix | 628-637 | 10 | |
Chain C: 11 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-41 | 19 | |
| α-helix | 46-60 | 15 | |
| α-helix | 71-87 | 17 | |
| α-helix | 92-94 | 3 | |
| β-strand | 102-108 | 7 | 4 |
| α-helix | 114-127 | 14 | |
| β-strand | 132-137 | 6 | 4 |
| α-helix | 144-154 | 11 | |
| β-strand | 159-160 | 2 | 4 |
| α-helix | 168-181 | 14 | |
| β-strand | 186-191 | 6 | 4 |
| α-helix | 199-212 | 14 | |
| β-strand | 216-222 | 7 | 4 |
| β-strand | 225 | 1 | 5 |
| α-helix | 229-239 | 11 | |
| β-strand | 242-248 | 7 | 4 |
| α-helix | 258-266 | 9 | |
| β-strand | 270-274 | 5 | 4 |
| β-strand | 282-284 | 3 | 4 |
| α-helix | 287-294 | 8 | |
Chain D: 14 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 334-351 | 18 | |
| α-helix | 356-370 | 15 | |
| α-helix | 378-397 | 20 | |
| α-helix | 405-414 | 10 | |
| β-strand | 419-425 | 7 | 6 |
| α-helix | 431-444 | 14 | |
| β-strand | 449-453 | 5 | 6 |
| α-helix | 461-475 | 15 | |
| α-helix | 478-481 | 4 | |
| β-strand | 487-490 | 4 | 6 |
| α-helix | 498-512 | 15 | |
| β-strand | 516-520 | 5 | 6 |
| α-helix | 529-542 | 14 | |
| β-strand | 546-552 | 7 | 6 |
| β-strand | 555 | 1 | 5 |
| α-helix | 558-572 | 15 | |
| β-strand | 584-588 | 5 | 6 |
| α-helix | 590-592 | 3 | |
| α-helix | 599-606 | 8 | |
| α-helix | 609-610 | 2 | |
| β-strand | 611-615 | 5 | 6 |
| β-strand | 623-624 | 2 | 6 |
| α-helix | 628-637 | 10 | |
Chain E: 12 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-41 | 19 | |
| α-helix | 46-60 | 15 | |
| α-helix | 71-87 | 17 | |
| α-helix | 92-94 | 3 | |
| α-helix | 96-97 | 2 | |
| β-strand | 102-108 | 7 | 7 |
| α-helix | 114-127 | 14 | |
| β-strand | 132-137 | 6 | 7 |
| α-helix | 144-154 | 11 | |
| β-strand | 159-160 | 2 | 7 |
| α-helix | 168-181 | 14 | |
| β-strand | 186-191 | 6 | 7 |
| α-helix | 199-212 | 14 | |
| β-strand | 216-222 | 7 | 7 |
| β-strand | 225 | 1 | 8 |
| α-helix | 229-239 | 11 | |
| β-strand | 242-248 | 7 | 7 |
| α-helix | 258-266 | 9 | |
| β-strand | 270-274 | 5 | 7 |
| β-strand | 282-284 | 3 | 7 |
| α-helix | 287-295 | 9 | |
Chain F: 13 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 333-351 | 19 | |
| α-helix | 356-369 | 14 | |
| α-helix | 379-397 | 19 | |
| α-helix | 405-414 | 10 | |
| β-strand | 419-424 | 6 | 9 |
| α-helix | 431-444 | 14 | |
| β-strand | 449-454 | 6 | 9 |
| α-helix | 461-475 | 15 | |
| α-helix | 478-481 | 4 | |
| β-strand | 487-490 | 4 | 9 |
| α-helix | 498-512 | 15 | |
| β-strand | 516-521 | 6 | 9 |
| α-helix | 529-542 | 14 | |
| β-strand | 546-552 | 7 | 9 |
| β-strand | 555 | 1 | 8 |
| α-helix | 558-572 | 15 | |
| β-strand | 584-588 | 5 | 9 |
| α-helix | 590-592 | 3 | |
| α-helix | 599-606 | 8 | |
| β-strand | 611-615 | 5 | 9 |
| β-strand | 623-624 | 2 | 9 |
| α-helix | 628-636 | 9 | |
Chain G: 12 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-41 | 19 | |
| α-helix | 46-59 | 14 | |
| α-helix | 72-87 | 16 | |
| α-helix | 92-94 | 3 | |
| α-helix | 96-97 | 2 | |
| β-strand | 102-108 | 7 | 10 |
| α-helix | 114-127 | 14 | |
| β-strand | 132-137 | 6 | 10 |
| α-helix | 144-154 | 11 | |
| β-strand | 159-160 | 2 | 10 |
| α-helix | 168-181 | 14 | |
| β-strand | 186-191 | 6 | 10 |
| α-helix | 199-212 | 14 | |
| β-strand | 216-222 | 7 | 10 |
| β-strand | 225 | 1 | 11 |
| α-helix | 229-239 | 11 | |
| β-strand | 242-248 | 7 | 10 |
| α-helix | 259-266 | 8 | |
| β-strand | 270-274 | 5 | 10 |
| β-strand | 282-284 | 3 | 10 |
| α-helix | 287-295 | 9 | |
Chain H: 13 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 333-351 | 19 | |
| α-helix | 356-369 | 14 | |
| α-helix | 378-397 | 20 | |
| α-helix | 405-415 | 11 | |
| β-strand | 419-424 | 6 | 12 |
| α-helix | 431-444 | 14 | |
| β-strand | 449-453 | 5 | 12 |
| α-helix | 461-472 | 12 | |
| α-helix | 473-475 | 3 | |
| β-strand | 487-490 | 4 | 12 |
| α-helix | 498-512 | 15 | |
| β-strand | 516-520 | 5 | 12 |
| α-helix | 529-542 | 14 | |
| β-strand | 546-552 | 7 | 12 |
| β-strand | 555 | 1 | 11 |
| α-helix | 558-572 | 15 | |
| β-strand | 584-588 | 5 | 12 |
| α-helix | 590-592 | 3 | |
| α-helix | 599-606 | 8 | |
| β-strand | 611-615 | 5 | 12 |
| β-strand | 623-624 | 2 | 12 |
| α-helix | 628-637 | 10 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Signal recognition particle 54 kDa protein | A, C, E, G | protein | 304 | Homo sapiens | P61011 (AlphaFold model) |
| Signal recognition particle receptor subunit alpha | B, D, F, H | protein | 315 | Homo sapiens | P08240 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>6Y32_1 Signal recognition particle 54 kDa protein (chains A, C, E, G)
MGHHHHHHMVLADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQL
RENVKSAIDLEEMASGLNKRKMIQHAVFKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGS
GKTTTCSKLAYYYQRKGWKTCLICADTFRAGAFDQLKQNATKARIPFYGSYTEMDPVIIA
SEGVEKFKNENFEIIIVDTSGRHKQEDSLFEEMLQVANAIQPDNIVYVMDASIGQACEAQ
AKAFKDKVDVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHIDDFEPFKTQPFIS
KLLG
Sequence of entity 2 (B, D, F, H), FASTA
>6Y32_2 Signal recognition particle receptor subunit alpha (chains B, D, F, H)
MGSLSREDMESVLDKMRDHLIAKNVAADIAVQLCESVANKLEGKVMGTFSTVTSTVKQAL
QESLVQILQPQRRVDMLRDIMDAQRRQRPYVVTFCGVNGVGKSTNLAKISFWLLENGFSV
LIAACDTFRAGAVEQLRTHTRRLSALHPPEKHGGRTMVQLFEKGYGKDAAGIAMEAIAFA
RNQGFDVVLVDTAGRMQDNAPLMTALAKLITVNTPDLVLFVGEALVGNEAVDQLVKFNRA
LADHSMAQTPRLIDGIVLTKFDTIDDKVGAAISMTYITSKPIVFVGTGQTYCDLRSLNAK
AVVAALMKAHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GNP | Phosphoaminophosphonic acid-guanylate ester | C10 H17 N6 O13 P3 | 8 |
| MG | Magnesium ion | Mg | 8 |
Water and common crystallization additives (SO4) are not listed.
Primary citation
Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia. Juaire, K.D., Lapouge, K., Becker, M.M.M. et al. Structure (2021) 29:15. DOI 10.1016/j.str.2020.09.008 · PubMed
Other PDB entries of the same protein (UniProt P61011 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1QB2 2.1 Å, Crystal structure of the conserved subdomain of human protein SRP54M at 2.1A resolution:…
- 6Y2Z 2.15 Å, NG domain of human SRP54
- 6Y30 2.65 Å, NG domain of human SRP54 T115A mutant
- 7QWQ 2.83 Å, Ternary complex of ribosome nascent chain with SRP and NAC
- 1MFQ 3.1 Å, Crystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition…
- 5L3Q 3.2 Å, Structure of the GTPase heterodimer of human SRP54 and SRalpha
- 7NFX 3.2 Å, Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A
- 6Y31 4.0 Å, NG domain of human SRP54 T117 deletion mutant
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