SMTL ID : 7eeb.1

Structure of the CatSpermasome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- BMA- BMA- BMA- BMA: beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA-BMA-BMA.1: 11 residues within 4Å: Chain E: N.90, T.92, F.93, I.119, V.121, N.122, D.124, E.129, W.131, A.304, N.305 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.122, E:N.305

7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.2: 4 residues within 4Å: Chain E: H.989, N.990, G.1015, N.1017 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain F: N.672, N.673 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain F: Y.138, N.356 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain H: N.91, S.94, P.95 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain H: P.247, M.248, T.249, I.250, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain H: Y.701, Q.702, D.859, C.919, N.920 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.702 NAG-NAG.16: 3 residues within 4Å: Chain H: R.756 Chain I: N.535, Q.551 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 8 residues within 4Å: Chain F: L.48, V.50, L.61, N.103, I.111, E.112, V.167, N.169 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 4 residues within 4Å: Chain F: P.71, L.94, F.176, N.178 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 5 residues within 4Å: Chain G: Q.624, N.627, S.629, P.663, V.665 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain H: N.143, S.145, I.147, H.213 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 6 residues within 4Å: Chain H: M.795, N.830, S.831, Q.835, K.892, H.894 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA.11: 6 residues within 4Å: Chain G: Y.119 Chain H: L.463, D.465, M.485, N.502, H.659 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Y.119 NAG-NAG-BMA-BMA-BMA.15: 8 residues within 4Å: Chain H: D.813, N.815, N.836, F.870, S.871, Y.872, N.888, N.891 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:F.870, H:N.836

1 x NAG- NAG- BMA- BMA- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA-BMA-BMA.12: 9 residues within 4Å: Chain H: E.74, K.96, N.565, Y.584, D.590, K.592, Y.593, Q.596, Q.598 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:Y.584 Hydrogen bonds: H:Q.596, H:Q.596

2 x NA: SODIUM ION(Non-functional Binders)

NA.17: 3 residues within 4Å: Chain A: L.804 Chain D: Q.236, D.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.804 NA.21: 4 residues within 4Å: Chain A: D.805, D.806 Chain C: D.227 Chain D: D.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.806

3 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.18: 8 residues within 4Å: Chain A: A.748, S.752, L.755 Chain D: L.196, I.197, L.269, G.274 Ligands: 9Z9.20 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.196, D:I.197, A:L.755 Hydrogen bonds: A:S.752 9Z9.19: 8 residues within 4Å: Chain A: P.683, W.684, L.687, L.729, R.736 Chain D: F.204, L.269 Ligands: 9Z9.20 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:F.204, D:L.269, A:P.683, A:P.683, A:W.684, A:L.729 Hydrogen bonds: A:R.736, A:R.736 9Z9.20: 8 residues within 4Å: Chain A: L.729, I.732, R.736, A.748 Chain D: L.196, V.203 Ligands: 9Z9.18, 9Z9.19 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.196, D:V.203, A:L.729, A:I.732, A:A.748

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.22: 2 residues within 4Å: Chain E: N.672, T.674 No protein-ligand interaction detected (PLIP) NAG.23: 2 residues within 4Å: Chain E: D.113, N.118 No protein-ligand interaction detected (PLIP) NAG.24: 1 residues within 4Å: Chain E: N.915 No protein-ligand interaction detected (PLIP) NAG.25: 3 residues within 4Å: Chain E: M.921, C.922, N.923 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:M.921, E:N.923 NAG.26: 2 residues within 4Å: Chain F: N.402, D.424 No protein-ligand interaction detected (PLIP) NAG.27: 1 residues within 4Å: Chain G: N.227 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.227 NAG.28: 1 residues within 4Å: Chain G: N.535 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.535 NAG.29: 3 residues within 4Å: Chain E: P.103 Chain G: D.467, N.469 No protein-ligand interaction detected (PLIP) NAG.30: 2 residues within 4Å: Chain H: N.749, R.752 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.749

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, S. et al., Structure of a mammalian sperm cation channel complex. Nature (2021)

Release Date

2021-07-28

Peptides

Enhanced green fluorescent protein,Cation channel sperm-associated protein 1: A
Cation channel sperm-associated protein 2: B
Cation channel sperm-associated protein 3: C
Cation channel sperm-associated protein 4: D
Cation channel sperm-associated protein subunit beta: E
Cation channel sperm-associated protein subunit gamma 2: F
Cation channel sperm-associated protein subunit delta: G
Cation channel sperm-associated protein subunit epsilon: H
Kazal-like domain-containing protein: I
Transmembrane protein 249: J
Transmembrane protein 262: K
Unknown: L
EF-hand calcium-binding domain-containing protein 9: M
Cation channel sperm-associated protein subunit zeta: N

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
L

J
J

K
M

L
N

M
I

N
K

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Enhanced green fluorescent protein,Cation channel sperm-associated protein 1

Cation channel sperm-associated protein 2

Cation channel sperm-associated protein 3

Cation channel sperm-associated protein 4

Cation channel sperm-associated protein subunit beta

Cation channel sperm-associated protein subunit gamma 2

Cation channel sperm-associated protein subunit delta

Cation channel sperm-associated protein subunit epsilon

Kazal-like domain-containing protein

Transmembrane protein 249

Transmembrane protein 262

Unknown

EF-hand calcium-binding domain-containing protein 9

Cation channel sperm-associated protein subunit zeta

Related Entries With Identical Sequence