SMTL ID : 7obq.1

SRP-SR at the distal site conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain E: K.77, T.78, S.95, D.117 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.78, E:S.95 MG.4: 3 residues within 4Å: Chain F: K.114, T.115 Ligands: GNP.3 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.115 MG.6: 4 residues within 4Å: Chain G: S.431, D.454, D.519 Ligands: GNP.5 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.431

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 20 residues within 4Å: Chain E: L.72, C.73, D.74, S.75, G.76, K.77, T.78, L.79, T.92, Q.93, T.94, S.95, G.120, N.180, K.181, D.183, S.247, A.248, K.249 Ligands: MG.1 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:D.74, E:D.74, E:S.75, E:G.76, E:T.78, E:L.79, E:T.92, E:T.94, E:S.95, E:G.120, E:N.180, E:K.181, E:A.248 Salt bridges: E:K.77, E:D.183 pi-Cation interactions: E:K.181

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.3: 22 residues within 4Å: Chain F: L.109, Q.110, G.111, G.113, K.114, T.115, T.116, K.120, D.138, R.141, Q.147, S.192, G.193, K.249, D.251, G.276, E.277 Chain G: N.426, G.427, R.457 Ligands: MG.4, GNP.5 21 PLIP interactions: 17 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:G.111, F:G.113, F:K.114, F:K.114, F:T.115, F:T.115, F:T.116, F:T.116, F:Q.147, F:Q.147, F:S.192, F:G.193, F:K.249, F:K.249, F:G.276, G:N.426, G:G.427, G:R.457 Salt bridges: F:D.251, F:E.277, G:R.457 GNP.5: 26 residues within 4Å: Chain F: Q.110, G.111, R.141, H.195 Chain G: N.426, V.428, G.429, K.430, S.431, T.432, N.433, K.436, D.454, R.457, Q.463, G.522, T.587, K.588, D.590, T.591, G.614, T.615, G.616, Q.617 Ligands: GNP.3, MG.6 23 PLIP interactions: 21 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:G.427, G:V.428, G:G.429, G:K.430, G:K.430, G:K.430, G:S.431, G:S.431, G:T.432, G:T.432, G:N.433, G:R.457, G:Q.463, G:G.522, G:T.587, G:K.588, G:K.588, G:G.616, G:Q.617, F:R.141 Salt bridges: G:D.590, F:R.141 pi-Cation interactions: G:K.588

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jomaa, A. et al., Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle. Cell Rep (2021)

Release Date

2021-07-21

Peptides

Signal recognition particle 19: B
EM14S01-3B_G0054400.mRNA.1.CDS.1: C
Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68: D
Signal recognition particle receptor subunit beta: E
Signal recognition particle 54 kDa protein: F
SRP receptor subunit alpha: G
Signal recognition particle subunit SRP72: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
q

C
s

D
u

E
v

F
x

G
y

H
z

Signal recognition particle 19

EM14S01-3B_G0054400.mRNA.1.CDS.1

Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68

Signal recognition particle receptor subunit beta

Signal recognition particle 54 kDa protein

SRP receptor subunit alpha

Signal recognition particle subunit SRP72

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