SMTL ID : 7ax3.1

CryoEM structure of the super-constricted two-start dynamin 1 filament

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-36-mer

Ligands

36 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)(Covalent)

GCP.1: 24 residues within 4Å: Chain A: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain B: D.211 Ligands: MG.2 Ligand excluded by PLIP GCP.3: 23 residues within 4Å: Chain A: D.211 Chain B: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.4 Ligand excluded by PLIP GCP.5: 24 residues within 4Å: Chain C: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain D: D.211 Ligands: MG.6 Ligand excluded by PLIP GCP.7: 23 residues within 4Å: Chain C: D.211 Chain D: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.8 Ligand excluded by PLIP GCP.9: 24 residues within 4Å: Chain E: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain F: D.211 Ligands: MG.10 Ligand excluded by PLIP GCP.11: 23 residues within 4Å: Chain E: D.211 Chain F: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.12 Ligand excluded by PLIP GCP.13: 24 residues within 4Å: Chain G: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain H: D.211 Ligands: MG.14 Ligand excluded by PLIP GCP.15: 23 residues within 4Å: Chain G: D.211 Chain H: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.16 Ligand excluded by PLIP GCP.17: 24 residues within 4Å: Chain I: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain J: D.211 Ligands: MG.18 Ligand excluded by PLIP GCP.19: 23 residues within 4Å: Chain I: D.211 Chain J: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.20 Ligand excluded by PLIP GCP.21: 24 residues within 4Å: Chain K: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain L: D.211 Ligands: MG.22 Ligand excluded by PLIP GCP.23: 23 residues within 4Å: Chain K: D.211 Chain L: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.24 Ligand excluded by PLIP GCP.25: 24 residues within 4Å: Chain M: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain N: D.211 Ligands: MG.26 Ligand excluded by PLIP GCP.27: 23 residues within 4Å: Chain M: D.211 Chain N: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.28 Ligand excluded by PLIP GCP.29: 23 residues within 4Å: Chain O: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.30 Ligand excluded by PLIP GCP.31: 24 residues within 4Å: Chain P: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain Q: D.211 Ligands: MG.32 Ligand excluded by PLIP GCP.33: 23 residues within 4Å: Chain P: D.211 Chain Q: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.34 Ligand excluded by PLIP GCP.35: 24 residues within 4Å: Chain R: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain S: D.211 Ligands: MG.36 Ligand excluded by PLIP GCP.37: 23 residues within 4Å: Chain R: D.211 Chain S: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.38 Ligand excluded by PLIP GCP.39: 24 residues within 4Å: Chain T: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain U: D.211 Ligands: MG.40 Ligand excluded by PLIP GCP.41: 23 residues within 4Å: Chain T: D.211 Chain U: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.42 Ligand excluded by PLIP GCP.43: 24 residues within 4Å: Chain V: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain W: D.211 Ligands: MG.44 Ligand excluded by PLIP GCP.45: 23 residues within 4Å: Chain V: D.211 Chain W: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.46 Ligand excluded by PLIP GCP.47: 24 residues within 4Å: Chain X: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain Y: D.211 Ligands: MG.48 Ligand excluded by PLIP GCP.49: 23 residues within 4Å: Chain X: D.211 Chain Y: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.50 Ligand excluded by PLIP GCP.51: 24 residues within 4Å: Chain 0: D.211 Chain Z: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.52 Ligand excluded by PLIP GCP.53: 23 residues within 4Å: Chain 0: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain Z: D.211 Ligands: MG.54 Ligand excluded by PLIP GCP.55: 24 residues within 4Å: Chain 1: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain 2: D.211 Ligands: MG.56 Ligand excluded by PLIP GCP.57: 23 residues within 4Å: Chain 1: D.211 Chain 2: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.58 Ligand excluded by PLIP GCP.59: 24 residues within 4Å: Chain 3: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain 4: D.211 Ligands: MG.60 Ligand excluded by PLIP GCP.61: 23 residues within 4Å: Chain 3: D.211 Chain 4: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.62 Ligand excluded by PLIP GCP.63: 23 residues within 4Å: Chain 5: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, S.61, V.64, T.65, P.138, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.64 Ligand excluded by PLIP GCP.65: 22 residues within 4Å: Chain 6: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.66 Ligand excluded by PLIP GCP.67: 22 residues within 4Å: Chain 7: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.68 Ligand excluded by PLIP GCP.69: 22 residues within 4Å: Chain 8: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.70 Ligand excluded by PLIP GCP.71: 22 residues within 4Å: Chain 9: Q.40, S.41, G.43, K.44, S.45, S.46, P.58, R.59, G.60, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.72 Ligand excluded by PLIP

36 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.45, T.65 Ligands: GCP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.65 MG.4: 4 residues within 4Å: Chain B: K.44, S.45, T.65 Ligands: GCP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.65 MG.6: 3 residues within 4Å: Chain C: S.45, T.65 Ligands: GCP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.65 MG.8: 4 residues within 4Å: Chain D: K.44, S.45, T.65 Ligands: GCP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.65 MG.10: 3 residues within 4Å: Chain E: S.45, T.65 Ligands: GCP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.65 MG.12: 4 residues within 4Å: Chain F: K.44, S.45, T.65 Ligands: GCP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.65 MG.14: 3 residues within 4Å: Chain G: S.45, T.65 Ligands: GCP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.65 MG.16: 4 residues within 4Å: Chain H: K.44, S.45, T.65 Ligands: GCP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.65 MG.18: 3 residues within 4Å: Chain I: S.45, T.65 Ligands: GCP.17 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.65 MG.20: 4 residues within 4Å: Chain J: K.44, S.45, T.65 Ligands: GCP.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.65 MG.22: 3 residues within 4Å: Chain K: S.45, T.65 Ligands: GCP.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.65 MG.24: 4 residues within 4Å: Chain L: K.44, S.45, T.65 Ligands: GCP.23 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.65 MG.26: 3 residues within 4Å: Chain M: S.45, T.65 Ligands: GCP.25 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.65 MG.28: 4 residues within 4Å: Chain N: K.44, S.45, T.65 Ligands: GCP.27 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.65 MG.30: 3 residues within 4Å: Chain O: S.45, T.65 Ligands: GCP.29 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.65 MG.32: 3 residues within 4Å: Chain P: S.45, T.65 Ligands: GCP.31 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.65 MG.34: 4 residues within 4Å: Chain Q: K.44, S.45, T.65 Ligands: GCP.33 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.65 MG.36: 3 residues within 4Å: Chain R: S.45, T.65 Ligands: GCP.35 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.65 MG.38: 4 residues within 4Å: Chain S: K.44, S.45, T.65 Ligands: GCP.37 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:T.65 MG.40: 3 residues within 4Å: Chain T: S.45, T.65 Ligands: GCP.39 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:T.65 MG.42: 4 residues within 4Å: Chain U: K.44, S.45, T.65 Ligands: GCP.41 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:T.65 MG.44: 3 residues within 4Å: Chain V: S.45, T.65 Ligands: GCP.43 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:T.65 MG.46: 4 residues within 4Å: Chain W: K.44, S.45, T.65 Ligands: GCP.45 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:T.65 MG.48: 3 residues within 4Å: Chain X: S.45, T.65 Ligands: GCP.47 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:T.65 MG.50: 4 residues within 4Å: Chain Y: K.44, S.45, T.65 Ligands: GCP.49 1 PLIP interactions: 1 interactions with chain Y Metal complexes: Y:T.65 MG.52: 3 residues within 4Å: Chain Z: S.45, T.65 Ligands: GCP.51 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:T.65 MG.54: 4 residues within 4Å: Chain 0: K.44, S.45, T.65 Ligands: GCP.53 1 PLIP interactions: 1 interactions with chain 0 Metal complexes: 0:T.65 MG.56: 3 residues within 4Å: Chain 1: S.45, T.65 Ligands: GCP.55 1 PLIP interactions: 1 interactions with chain 1 Metal complexes: 1:T.65 MG.58: 4 residues within 4Å: Chain 2: K.44, S.45, T.65 Ligands: GCP.57 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:T.65 MG.60: 3 residues within 4Å: Chain 3: S.45, T.65 Ligands: GCP.59 1 PLIP interactions: 1 interactions with chain 3 Metal complexes: 3:T.65 MG.62: 4 residues within 4Å: Chain 4: K.44, S.45, T.65 Ligands: GCP.61 1 PLIP interactions: 1 interactions with chain 4 Metal complexes: 4:T.65 MG.64: 3 residues within 4Å: Chain 5: S.45, T.65 Ligands: GCP.63 1 PLIP interactions: 1 interactions with chain 5 Metal complexes: 5:T.65 MG.66: 4 residues within 4Å: Chain 6: K.44, S.45, T.65 Ligands: GCP.65 1 PLIP interactions: 1 interactions with chain 6 Metal complexes: 6:T.65 MG.68: 4 residues within 4Å: Chain 7: K.44, S.45, T.65 Ligands: GCP.67 1 PLIP interactions: 1 interactions with chain 7 Metal complexes: 7:T.65 MG.70: 4 residues within 4Å: Chain 8: K.44, S.45, T.65 Ligands: GCP.69 1 PLIP interactions: 1 interactions with chain 8 Metal complexes: 8:T.65 MG.72: 4 residues within 4Å: Chain 9: K.44, S.45, T.65 Ligands: GCP.71 1 PLIP interactions: 1 interactions with chain 9 Metal complexes: 9:T.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., CryoEM structure of the super-constricted two-start dynamin 1 filament. Nat Commun (2021)

Release Date

2021-11-10

Peptides

Dynamin-1: ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C2

B
D2

C
A2

D
B2

E
A

F
B

G
C

H
D

I
E

J
F

K
G

L
H

M
I

N
J

O
K

P
L

Q
M

R
N

S
O

T
P

U
Q

V
R

W
S

X
T

Y
U

Z
V

0
W

1
X

2
Y

3
Z

4
E2

5
F2

6
G2

7
H2

8
I2

9
J2

Dynamin-1

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