SMTL ID : 8rmk.1

Cryo-EM structure of human CALHM2 in complex with synthetic nanobody SbC2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-11-11-mer

Ligands

11 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.1: 11 residues within 4Å: Chain A: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.112, A:V.113, A:V.113, A:L.192, A:V.196, A:V.200 PLC.2: 11 residues within 4Å: Chain C: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.112, C:V.113, C:V.113, C:L.192, C:V.196, C:V.200 PLC.3: 11 residues within 4Å: Chain D: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.112, D:V.113, D:V.113, D:L.192, D:V.196, D:V.200 PLC.4: 11 residues within 4Å: Chain E: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:A.112, E:V.113, E:V.113, E:L.192, E:V.196, E:V.200 PLC.5: 11 residues within 4Å: Chain F: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:A.112, F:V.113, F:V.113, F:L.192, F:V.196, F:V.200 PLC.6: 11 residues within 4Å: Chain G: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:A.112, G:V.113, G:V.113, G:L.192, G:V.196, G:V.200 PLC.7: 11 residues within 4Å: Chain H: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:A.112, H:V.113, H:V.113, H:L.192, H:V.196, H:V.200 PLC.8: 11 residues within 4Å: Chain I: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:A.112, I:V.113, I:V.113, I:L.192, I:V.196, I:V.200 PLC.9: 11 residues within 4Å: Chain J: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:A.112, J:V.113, J:V.113, J:L.192, J:V.196, J:V.200 PLC.10: 11 residues within 4Å: Chain K: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:A.112, K:V.113, K:V.113, K:L.192, K:V.196, K:V.200 PLC.11: 11 residues within 4Å: Chain L: S.105, S.106, G.109, A.112, V.113, V.116, L.192, V.196, V.200, T.203, K.207 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:A.112, L:V.113, L:V.113, L:L.192, L:V.196, L:V.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drozdzyk, K. et al., Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs. Elife (2024)

Release Date

2024-06-19

Peptides

Calcium homeostasis modulator protein 2: ACDEFGHIJKL
Synthetic nanobody SbC2: BMNOPQRSTUV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

D
C

E
D

F
E

G
F

H
G

I
H

J
I

K
J

L
K

B
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

Membrane

We predict this structure to be a membrane protein.
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Calcium homeostasis modulator protein 2

Synthetic nanobody SbC2

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