5M73: Human SRP S domain with SRP72 RNA-binding domain
Structure of the human SRP S domain with SRP72 RNA-binding domain. Determined by X-ray diffraction at 3.4 Å resolution. Released 7 Dec 2016.
- Method
- X-ray diffraction
- Resolution
- 3.4 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 12,128
- Mol. weight
- 209.24 kDa
- Ligands
- MG
- Released
- 7 Dec 2016
Explore 5M73 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5M73 contains 30 α-helices and 18 β-strands across 6 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 B: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| β-strand | 16-18 | 3 | 1 |
| α-helix | 20-23 | 4 | |
| β-strand | 24 | 1 | 2 |
| α-helix | 29-31 | 3 | |
| β-strand | 41 | 1 | 2 |
| α-helix | 46-56 | 11 | |
| β-strand | 60-63 | 4 | 1 |
| β-strand | 81-84 | 4 | 1 |
| β-strand | 87 | 1 | 3 |
| β-strand | 93 | 1 | 3 |
| α-helix | 101-111 | 11 | |
| α-helix | 112-114 | 3 | |
Chain C: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-72 | 11 | |
| α-helix | 80-97 | 18 | |
| α-helix | 116-120 | 5 | |
| α-helix | 124-145 | 22 | |
| α-helix | 151-172 | 22 | |
| α-helix | 180-200 | 21 | |
| α-helix | 204-222 | 19 | |
| α-helix | 227-251 | 25 | |
Chain D: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 563-566 | 4 | |
| α-helix | 590-602 | 13 | |
Chain F: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-18 | 3 | 4 |
| α-helix | 20-23 | 4 | |
| β-strand | 24 | 1 | 5 |
| β-strand | 41 | 1 | 5 |
| α-helix | 46-54 | 9 | |
| β-strand | 60-67 | 8 | 4 |
| α-helix | 76-78 | 3 | |
| β-strand | 79-84 | 6 | 4 |
| β-strand | 87 | 1 | 6 |
| β-strand | 93 | 1 | 6 |
| α-helix | 101-116 | 16 | |
Chain G: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 58 | 1 | 7 |
| α-helix | 62-72 | 11 | |
| α-helix | 75-77 | 3 | |
| α-helix | 80-97 | 18 | |
| β-strand | 103-104 | 2 | 8 |
| β-strand | 107-108 | 2 | 8 |
| α-helix | 116-120 | 5 | |
| α-helix | 123-145 | 23 | |
| α-helix | 151-173 | 23 | |
| β-strand | 178 | 1 | 7 |
| α-helix | 180-200 | 21 | |
| α-helix | 204-224 | 21 | |
| α-helix | 227-249 | 23 | |
Chain H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 590-602 | 13 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Human gene for small cytoplasmic 7SL RNA (7L30.1) | A, E | RNA | 145 | Homo sapiens | |
| Signal recognition particle 19 kDa protein | B, F | protein | 128 | Homo sapiens | P09132 (AlphaFold model) |
| Signal recognition particle subunit SRP68 | C, G | protein | 203 | Homo sapiens | Q9UHB9 (AlphaFold model) |
| Signal recognition particle subunit SRP72 | D, H | protein | 158 | Homo sapiens | O76094 (AlphaFold model) |
Sequence of entity 1 (A, E), FASTA
>5M73_1 Human gene for small cytoplasmic 7SL RNA (7L30.1) (chains A, E)
GGGUGUCCGCACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAG
GUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUG
CUGAUCAGUAGUGGGAUCGCGCCUA
Sequence of entity 2 (B, F), FASTA
>5M73_2 Signal recognition particle 19 kDa protein (chains B, F)
MACAAARSPADQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNV
FLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ
LEHHHHHH
Sequence of entity 3 (C, G), FASTA
>5M73_3 Signal recognition particle subunit SRP68 (chains C, G)
MGHHHHHHLEILQIIKESQQQHGLRHGDFQRYRGYCSRRQRRLRKTLNFKMGNRHKFTGK
KVTEDLLTDNRYLLLVLMDAERAWSYAMQLKQEANTEPRKRFHLLSRLRKAVKHAEELER
LCESNRVDAKTKLEAQAYTAYLSGMLRFEHQEWKAAIEAFNKCKTIYEKLASAFTEEQAV
LYNQRVEEISPNIRYCAYNIGDQ
Sequence of entity 4 (D, H), FASTA
>5M73_4 Signal recognition particle subunit SRP72 (chains D, H)
MGSLKVDVEALENSAGATYIRKKGGKVTGDSQPKEQGQGDLKKKKKKKKGKLPKNYDPKV
TPDPERWLPMRERSYYRGRKKGKKKDQIGKGTQGATAGASSELDASKTVSSPPTSPRPGS
AATVSASTSNIIPPRHQKPAGAPATKKKQQQKHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 45 |
Water and common crystallization additives (GOL, K) are not listed.
Primary citation
Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction. Becker, M.M., Lapouge, K., Segnitz, B. et al. Nucleic Acids Res (2017) 45:470-481. DOI 10.1093/nar/gkw1124 · PubMed
Other PDB entries of the same protein (UniProt P09132 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1JID 1.8 Å, Human SRP19 in complex with helix 6 of Human SRP RNA
- 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…
- 7NFX 3.2 Å, Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A
- 4P3E 3.5 Å, Structure of the human SRP S domain
- 3KTV 3.8 Å, Crystal structure of the human SRP19/S-domain SRP RNA complex
- 2J37 8.7 Å, Model of mammalian srp bound to 80S rncs
- 1RY1 12.0 Å, Structure of the signal recognition particle interacting with the elongation-arrested…
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