SMTL ID : 9iuy.1

Cryo-EM structure of mouse heavy-chain apoferritin resolved at 1.51 Angstroms

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

32 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.28, A:E.63, A:H.66, H2O.1, H2O.2 MG.4: 6 residues within 4Å: Chain A: D.132, E.135 Chain F: D.132, E.135 Chain T: D.132, E.135 5 PLIP interactions: 1 interactions with chain T, 1 interactions with chain F, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: T:E.135, F:E.135, A:E.135, H2O.2, H2O.28 MG.5: 4 residues within 4Å: Chain B: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.28, B:E.63, B:H.66, H2O.6, H2O.7 MG.8: 6 residues within 4Å: Chain B: D.132, E.135 Chain U: D.132, E.135 Chain W: D.132, E.135 5 PLIP interactions: 1 interactions with chain U, 1 interactions with chain W, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: U:E.135, W:E.135, B:E.135, H2O.7, H2O.107 MG.9: 4 residues within 4Å: Chain C: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.28, C:E.63, C:H.66, H2O.11, H2O.12 MG.12: 6 residues within 4Å: Chain C: D.132, E.135 Chain K: D.132, E.135 Chain M: D.132, E.135 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain K, 1 interactions with chain M, 2 Ligand-Water interactions Metal complexes: C:E.135, K:E.135, M:E.135, H2O.12, H2O.65 MG.13: 4 residues within 4Å: Chain D: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.28, D:E.63, D:H.66, H2O.16, H2O.18 MG.15: 6 residues within 4Å: Chain D: D.132, E.135 Chain L: D.132, E.135 Chain V: D.132, E.135 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain V, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: D:E.135, V:E.135, L:E.135, H2O.18, H2O.60 MG.16: 4 residues within 4Å: Chain E: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.28, E:E.63, E:H.66, H2O.22, H2O.23 MG.19: 6 residues within 4Å: Chain E: D.132, E.135 Chain G: D.132, E.135 Chain Q: D.132, E.135 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain Q, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: E:E.135, Q:E.135, G:E.135, H2O.23, H2O.86 MG.20: 4 residues within 4Å: Chain F: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.28, F:E.63, F:H.66, H2O.27, H2O.28 MG.22: 4 residues within 4Å: Chain G: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.28, G:E.63, G:H.66, H2O.32, H2O.33 MG.24: 4 residues within 4Å: Chain H: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.28, H:E.63, H:H.66, H2O.38, H2O.39 MG.26: 6 residues within 4Å: Chain H: D.132, E.135 Chain N: D.132, E.135 Chain S: D.132, E.135 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain N, 1 interactions with chain S, 2 Ligand-Water interactions Metal complexes: H:E.135, N:E.135, S:E.135, H2O.39, H2O.97 MG.27: 4 residues within 4Å: Chain I: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.28, I:E.63, I:H.66, H2O.43, H2O.44 MG.29: 6 residues within 4Å: Chain I: D.132, E.135 Chain P: D.132, E.135 Chain X: D.132, E.135 5 PLIP interactions: 1 interactions with chain X, 1 interactions with chain I, 1 interactions with chain P, 2 Ligand-Water interactions Metal complexes: X:E.135, I:E.135, P:E.135, H2O.44, H2O.123 MG.30: 4 residues within 4Å: Chain J: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.28, J:E.63, J:H.66, H2O.48, H2O.49 MG.32: 6 residues within 4Å: Chain J: D.132, E.135 Chain O: D.132, E.135 Chain R: D.132, E.135 5 PLIP interactions: 1 interactions with chain O, 1 interactions with chain R, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: O:E.135, R:E.135, J:E.135, H2O.76, H2O.91 MG.33: 4 residues within 4Å: Chain K: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.28, K:E.63, K:H.66, H2O.53, H2O.55 MG.35: 4 residues within 4Å: Chain L: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.28, L:E.63, L:H.66, H2O.59, H2O.60 MG.38: 4 residues within 4Å: Chain M: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.28, M:E.63, M:H.66, H2O.64, H2O.65 MG.40: 4 residues within 4Å: Chain N: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.28, N:E.63, N:H.66, H2O.69, H2O.70 MG.42: 4 residues within 4Å: Chain O: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.28, O:E.63, O:H.66, H2O.74, H2O.76 MG.44: 4 residues within 4Å: Chain P: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.28, P:E.63, P:H.66, H2O.80, H2O.81 MG.47: 4 residues within 4Å: Chain Q: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.28, Q:E.63, Q:H.66, H2O.85, H2O.86 MG.49: 4 residues within 4Å: Chain R: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.28, R:E.63, R:H.66, H2O.90, H2O.91 MG.51: 4 residues within 4Å: Chain S: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.28, S:E.63, S:H.66, H2O.95, H2O.97 MG.53: 4 residues within 4Å: Chain T: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.28, T:E.63, T:H.66, H2O.101, H2O.102 MG.55: 4 residues within 4Å: Chain U: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.28, U:E.63, U:H.66, H2O.106, H2O.107 MG.57: 4 residues within 4Å: Chain V: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.28, V:E.63, V:H.66, H2O.111, H2O.113 MG.59: 4 residues within 4Å: Chain W: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.28, W:E.63, W:H.66, H2O.117, H2O.118 MG.61: 4 residues within 4Å: Chain X: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.28, X:E.63, X:H.66, H2O.122, H2O.123

24 x K: POTASSIUM ION(Non-covalent)

K.2: 2 residues within 4Å: Chain A: Y.41, D.93 Ligand excluded by PLIP K.6: 2 residues within 4Å: Chain B: Y.41, D.93 Ligand excluded by PLIP K.10: 2 residues within 4Å: Chain C: Y.41, D.93 Ligand excluded by PLIP K.14: 2 residues within 4Å: Chain D: Y.41, D.93 Ligand excluded by PLIP K.17: 2 residues within 4Å: Chain E: Y.41, D.93 Ligand excluded by PLIP K.21: 2 residues within 4Å: Chain F: Y.41, D.93 Ligand excluded by PLIP K.23: 2 residues within 4Å: Chain G: Y.41, D.93 Ligand excluded by PLIP K.25: 2 residues within 4Å: Chain H: Y.41, D.93 Ligand excluded by PLIP K.28: 2 residues within 4Å: Chain I: Y.41, D.93 Ligand excluded by PLIP K.31: 2 residues within 4Å: Chain J: Y.41, D.93 Ligand excluded by PLIP K.34: 2 residues within 4Å: Chain K: Y.41, D.93 Ligand excluded by PLIP K.36: 2 residues within 4Å: Chain L: Y.41, D.93 Ligand excluded by PLIP K.39: 2 residues within 4Å: Chain M: Y.41, D.93 Ligand excluded by PLIP K.41: 2 residues within 4Å: Chain N: Y.41, D.93 Ligand excluded by PLIP K.43: 2 residues within 4Å: Chain O: Y.41, D.93 Ligand excluded by PLIP K.45: 2 residues within 4Å: Chain P: Y.41, D.93 Ligand excluded by PLIP K.48: 2 residues within 4Å: Chain Q: Y.41, D.93 Ligand excluded by PLIP K.50: 2 residues within 4Å: Chain R: Y.41, D.93 Ligand excluded by PLIP K.52: 2 residues within 4Å: Chain S: Y.41, D.93 Ligand excluded by PLIP K.54: 2 residues within 4Å: Chain T: Y.41, D.93 Ligand excluded by PLIP K.56: 2 residues within 4Å: Chain U: Y.41, D.93 Ligand excluded by PLIP K.58: 2 residues within 4Å: Chain V: Y.41, D.93 Ligand excluded by PLIP K.60: 2 residues within 4Å: Chain W: Y.41, D.93 Ligand excluded by PLIP K.62: 2 residues within 4Å: Chain X: Y.41, D.93 Ligand excluded by PLIP

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

FE.3: 8 residues within 4Å: Chain A: L.170, H.174 Chain D: L.170, H.174 Chain G: L.170, H.174 Chain H: L.170, H.174 No protein-ligand interaction detected (PLIP) FE.7: 8 residues within 4Å: Chain B: L.170, H.174 Chain I: L.170, H.174 Chain J: L.170, H.174 Chain K: L.170, H.174 No protein-ligand interaction detected (PLIP) FE.11: 8 residues within 4Å: Chain C: L.170, H.174 Chain F: L.170, H.174 Chain U: L.170, H.174 Chain V: L.170, H.174 No protein-ligand interaction detected (PLIP) FE.18: 8 residues within 4Å: Chain E: L.170, H.174 Chain T: L.170, H.174 Chain W: L.170, H.174 Chain X: L.170, H.174 No protein-ligand interaction detected (PLIP) FE.37: 8 residues within 4Å: Chain L: L.170, H.174 Chain M: L.170, H.174 Chain N: L.170, H.174 Chain O: L.170, H.174 No protein-ligand interaction detected (PLIP) FE.46: 8 residues within 4Å: Chain P: L.170, H.174 Chain Q: L.170, H.174 Chain R: L.170, H.174 Chain S: L.170, H.174 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C.H. et al., Cryo-EM structure of mouse heavy-chain apoferritin resolved at 1.51 Angstroms. To Be Published

Release Date

2024-08-21

Peptides

Ferritin heavy chain: 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

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