SMTL ID : 4bzi.1

The structure of the COPII coat assembled on membranes

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 23.00 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.56, C.61, C.80, C.83 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.56, A:C.61, A:C.80, A:C.83 ZN.4: 4 residues within 4Å: Chain C: C.56, C.61, C.80, C.83 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.56, C:C.61, C:C.80, C:C.83 ZN.5: 4 residues within 4Å: Chain D: C.231, C.234, C.253, C.256 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.231, D:C.234, D:C.253, D:C.256 ZN.6: 4 residues within 4Å: Chain F: C.56, C.61, C.80, C.83 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.56, F:C.61, F:C.80, F:C.83 ZN.11: 4 residues within 4Å: Chain I: C.231, C.234, C.253, C.256 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.231, I:C.234, I:C.253, I:C.256 ZN.12: 4 residues within 4Å: Chain J: C.231, C.234, C.253, C.256 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.231, J:C.234, J:C.253, J:C.256

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

GNP.2: 23 residues within 4Å: Chain A: R.722 Chain B: L.31, D.32, N.33, A.34, G.35, K.36, T.37, T.38, T.50, L.51, P.53, T.54, G.75, G.76, N.132, K.133, D.135, A.136, S.172, V.173, V.174 Ligands: MG.3 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.33, B:A.34, B:G.35, B:K.36, B:K.36, B:T.37, B:T.37, B:T.38, B:T.38, B:T.50, B:T.50, B:T.54, B:L.74, B:G.76, B:N.132, B:K.133, B:V.173, B:V.174, A:R.722, A:R.722 Salt bridges: B:D.135, A:R.722 GNP.7: 23 residues within 4Å: Chain C: R.722 Chain G: L.31, D.32, N.33, A.34, G.35, K.36, T.37, T.38, T.50, L.51, P.53, T.54, G.75, G.76, N.132, K.133, D.135, A.136, S.172, V.173, V.174 Ligands: MG.8 22 PLIP interactions: 19 interactions with chain G, 3 interactions with chain C Hydrogen bonds: G:N.33, G:A.34, G:G.35, G:K.36, G:K.36, G:T.37, G:T.37, G:T.38, G:T.38, G:T.50, G:T.50, G:T.54, G:L.74, G:G.76, G:N.132, G:K.133, G:V.173, G:V.174, C:R.722, C:R.722 Salt bridges: G:D.135, C:R.722 GNP.9: 23 residues within 4Å: Chain F: R.722 Chain H: L.31, D.32, N.33, A.34, G.35, K.36, T.37, T.38, T.50, L.51, P.53, T.54, G.75, G.76, N.132, K.133, D.135, A.136, S.172, V.173, V.174 Ligands: MG.10 21 PLIP interactions: 18 interactions with chain H, 3 interactions with chain F Hydrogen bonds: H:N.33, H:A.34, H:G.35, H:K.36, H:K.36, H:T.37, H:T.37, H:T.38, H:T.50, H:T.50, H:T.54, H:L.74, H:G.76, H:N.132, H:K.133, H:V.173, H:V.174, F:R.722, F:R.722 Salt bridges: H:D.135, F:R.722

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: T.37, T.54 Ligands: GNP.2 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.37, B:T.54 MG.8: 3 residues within 4Å: Chain G: T.37, T.54 Ligands: GNP.7 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.37, G:T.54 MG.10: 3 residues within 4Å: Chain H: T.37, T.54 Ligands: GNP.9 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.37, H:T.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zanetti, G. et al., The Structure of the Copii Transport-Vesicle Coat Assembled on Membranes. Elife (2013)

Release Date

2013-09-18

Peptides

SEC23P: ACF
SAR1P: BGH
SEC24P: DIJ
SEC24P: EKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

F
G

B
B

G
J

H
K

D
E

I
L

J
M

E
F

K
N

L
O

SEC23P

SAR1P

SEC24P

SEC24P

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