SMTL ID : 8emq.1

Mouse apoferritin heavy chain with zinc determined using single-particle cryo-EM with Apollo camera.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.23, A:E.58, A:H.61, H2O.1, H2O.4 ZN.3: 4 residues within 4Å: Chain B: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.23, B:E.58, B:H.61, H2O.6, H2O.6 ZN.4: 4 residues within 4Å: Chain C: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.23, C:E.58, C:H.61, H2O.11, H2O.11 ZN.5: 4 residues within 4Å: Chain D: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.23, D:E.58, D:H.61, H2O.15, H2O.16 ZN.7: 4 residues within 4Å: Chain E: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.23, E:E.58, E:H.61, H2O.20, H2O.21 ZN.8: 4 residues within 4Å: Chain F: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.23, F:E.58, F:H.61, H2O.25, H2O.25 ZN.9: 4 residues within 4Å: Chain G: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.23, G:E.58, G:H.61, H2O.30, H2O.30 ZN.11: 4 residues within 4Å: Chain H: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.23, H:E.58, H:H.61, H2O.35, H2O.35 ZN.13: 4 residues within 4Å: Chain I: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.23, I:E.58, I:H.61, H2O.39, H2O.40 ZN.15: 4 residues within 4Å: Chain J: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.23, J:E.58, J:H.61, H2O.44, H2O.45 ZN.16: 4 residues within 4Å: Chain K: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.23, K:E.58, K:H.61, H2O.49, H2O.49 ZN.17: 4 residues within 4Å: Chain L: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.23, L:E.58, L:H.61, H2O.54, H2O.54 ZN.18: 4 residues within 4Å: Chain M: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.23, M:E.58, M:H.61, H2O.58, H2O.59 ZN.19: 4 residues within 4Å: Chain N: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.23, N:E.58, N:H.61, H2O.63, H2O.64 ZN.20: 4 residues within 4Å: Chain O: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.23, O:E.58, O:H.61, H2O.68, H2O.68 ZN.21: 4 residues within 4Å: Chain P: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.23, P:E.58, P:H.61, H2O.73, H2O.73 ZN.22: 4 residues within 4Å: Chain Q: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.23, Q:E.58, Q:H.61, H2O.77, H2O.78 ZN.23: 4 residues within 4Å: Chain R: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.23, R:E.58, R:H.61, H2O.82, H2O.83 ZN.25: 4 residues within 4Å: Chain S: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.23, S:E.58, S:H.61, H2O.87, H2O.87 ZN.26: 4 residues within 4Å: Chain T: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.23, T:E.58, T:H.61, H2O.92, H2O.92 ZN.27: 4 residues within 4Å: Chain U: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.23, U:E.58, U:H.61, H2O.96, H2O.97 ZN.28: 4 residues within 4Å: Chain V: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.23, V:E.58, V:H.61, H2O.101, H2O.102 ZN.29: 4 residues within 4Å: Chain W: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.23, W:E.58, W:H.61, H2O.106, H2O.107 ZN.30: 4 residues within 4Å: Chain X: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.23, X:E.58, X:H.61, H2O.111, H2O.111

6 x FE: FE (III) ION(Non-covalent)

FE.2: 7 residues within 4Å: Chain A: L.165, H.169 Chain B: L.165, H.169 Chain C: L.165, H.169 Chain H: H.169 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain H Metal complexes: A:H.169, B:H.169, C:H.169, H:H.169 FE.6: 7 residues within 4Å: Chain D: L.165, H.169 Chain E: L.165, H.169 Chain M: H.169 Chain N: L.165, H.169 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain N, 1 interactions with chain D, 1 interactions with chain M Metal complexes: E:H.169, N:H.169, D:H.169, M:H.169 FE.10: 7 residues within 4Å: Chain F: H.169 Chain G: L.165, H.169 Chain V: L.165, H.169 Chain X: L.165, H.169 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain V, 1 interactions with chain F, 1 interactions with chain X Metal complexes: G:H.169, V:H.169, F:H.169, X:H.169 FE.12: 7 residues within 4Å: Chain I: L.165, H.169 Chain K: L.165, H.169 Chain O: H.169 Chain W: L.165, H.169 4 PLIP interactions: 1 interactions with chain O, 1 interactions with chain W, 1 interactions with chain I, 1 interactions with chain K Metal complexes: O:H.169, W:H.169, I:H.169, K:H.169 FE.14: 7 residues within 4Å: Chain J: L.165, H.169 Chain L: L.165, H.169 Chain P: L.165, H.169 Chain Q: H.169 4 PLIP interactions: 1 interactions with chain J, 1 interactions with chain P, 1 interactions with chain L, 1 interactions with chain Q Metal complexes: J:H.169, P:H.169, L:H.169, Q:H.169 FE.24: 7 residues within 4Å: Chain R: L.165, H.169 Chain S: H.169 Chain T: L.165, H.169 Chain U: L.165, H.169 4 PLIP interactions: 1 interactions with chain R, 1 interactions with chain T, 1 interactions with chain U, 1 interactions with chain S Metal complexes: R:H.169, T:H.169, U:H.169, S:H.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, R. et al., Characterizing the resolution and throughput of the Apollo direct electron detector. J Struct Biol X (2023)

Release Date

2022-12-21

Peptides

Ferritin heavy chain, N-terminally processed: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Ferritin heavy chain, N-terminally processed

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