SMTL ID : 6k7y.1

Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

hetero-8-8-2-2-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.192 Chain B: E.192 Chain C: E.192 Chain D: E.192 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:E.192, D:E.192, D:E.192, C:E.192, A:E.192 CA.14: 4 residues within 4Å: Chain K: E.192 Chain L: E.192 Chain M: E.192 Chain N: E.192 5 PLIP interactions: 1 interactions with chain K, 2 interactions with chain N, 1 interactions with chain L, 1 interactions with chain M Metal complexes: K:E.192, N:E.192, N:E.192, L:E.192, M:E.192

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 18 residues within 4Å: Chain A: V.163, Y.170, T.173, A.205, Y.209, M.212, T.213, R.225, Q.226, L.229, F.230 Chain C: F.175 Chain F: K.15, L.20, F.24 Chain G: F.30 Ligands: PLX.3, PLX.11 12 PLIP interactions: 7 interactions with chain A, 2 interactions with chain G, 2 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: A:V.163, A:Y.170, A:A.205, G:F.30, G:F.30, F:F.24, C:F.175 Hydrogen bonds: A:Q.226, A:Q.226 Salt bridges: A:R.225, A:K.233, F:K.15 CDL.5: 14 residues within 4Å: Chain B: R.159, Y.209, M.212, T.213, R.225, Q.226, L.229, F.230, K.233 Chain G: K.15, L.20, F.24 Ligands: PLX.4, PLX.6 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain B Hydrophobic interactions: G:L.20, G:F.24 Hydrogen bonds: B:Q.226 Salt bridges: B:R.225, B:K.233, B:K.233 CDL.8: 17 residues within 4Å: Chain C: M.204, A.205, Y.209, M.212, T.213, R.225, Q.226, L.229, F.230 Chain D: F.175 Chain E: F.18, L.20, F.24, L.31 Chain F: I.37 Ligands: PLX.9, PLX.10 14 PLIP interactions: 4 interactions with chain C, 7 interactions with chain E, 1 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: C:A.205, E:F.18, E:L.20, E:L.20, E:L.20, E:F.24, E:L.31, F:I.37, D:F.175, D:F.175 Hydrogen bonds: C:Q.226, C:Q.226 Salt bridges: C:R.225, E:K.15 CDL.13: 17 residues within 4Å: Chain B: F.175 Chain D: Y.170, I.198, Y.209, M.212, T.213, R.225, L.229, F.230, K.233 Chain H: K.15, F.18, L.20, V.23, F.24, V.27 Ligands: PLX.12 10 PLIP interactions: 6 interactions with chain H, 4 interactions with chain D Hydrophobic interactions: H:F.18, H:L.20, H:V.23, H:F.24, H:V.27, D:I.198, D:K.233 Salt bridges: H:K.15, D:R.225, D:K.233 CDL.15: 18 residues within 4Å: Chain K: V.163, G.166, T.173, M.204, A.205, Y.209, M.212, T.213, R.225, Q.226, L.229 Chain M: F.175 Chain P: K.15, F.18, L.20, F.24, L.31 Ligands: PLX.16 10 PLIP interactions: 5 interactions with chain P, 4 interactions with chain K, 1 interactions with chain M Hydrophobic interactions: P:F.18, P:L.20, P:F.24, P:L.31, K:V.163, M:F.175 Salt bridges: P:K.15, K:R.225, K:K.233 Hydrogen bonds: K:Q.226 CDL.18: 19 residues within 4Å: Chain K: F.175 Chain L: R.159, M.204, A.208, Y.209, M.212, T.213, R.225, Q.226, L.229, F.230, K.233 Chain Q: K.15, L.20, V.23, F.24, L.31 Ligands: PLX.17, PLX.19 12 PLIP interactions: 5 interactions with chain Q, 6 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: Q:L.20, Q:V.23, Q:F.24, Q:L.31, L:A.208, K:F.175 Salt bridges: Q:K.15, L:R.225, L:K.233, L:K.233 Hydrogen bonds: L:R.159, L:Q.226 CDL.21: 16 residues within 4Å: Chain M: M.204, Y.209, M.212, T.213, R.225, Q.226, L.229, F.230 Chain N: F.175 Chain O: K.15, F.18, L.20, F.24, L.31 Ligands: PLX.22, PLX.23 10 PLIP interactions: 5 interactions with chain O, 1 interactions with chain N, 4 interactions with chain M Hydrophobic interactions: O:F.18, O:L.20, O:F.24, O:L.31, N:F.175 Salt bridges: O:K.15, M:R.225, M:K.233 Hydrogen bonds: M:Q.226, M:Q.226 CDL.25: 20 residues within 4Å: Chain L: F.175 Chain N: Y.170, I.198, G.201, A.205, Y.209, M.212, T.213, R.225, Q.226, L.229, F.230, K.233 Chain R: K.15, F.18, L.20, V.23, F.24, V.27 Ligands: PLX.26 16 PLIP interactions: 7 interactions with chain R, 8 interactions with chain N, 1 interactions with chain L Hydrophobic interactions: R:K.15, R:F.18, R:L.20, R:V.23, R:F.24, R:V.27, N:Y.170, N:I.198, N:A.205, N:K.233, L:F.175 Salt bridges: R:K.15, N:R.159, N:R.225, N:K.233 Hydrogen bonds: N:Q.226

16 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)

PLX.3: 14 residues within 4Å: Chain A: V.163, L.164, G.166, G.167, M.171, S.202, M.206, Y.209, Y.217, Y.219, Q.226 Chain B: F.210, E.216 Ligands: CDL.2 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.163, A:L.164, A:Y.209, A:Y.219, B:F.210 Hydrogen bonds: A:Y.217, A:Y.219, A:Y.219 PLX.4: 3 residues within 4Å: Chain A: W.183, W.184 Ligands: CDL.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.183 PLX.6: 14 residues within 4Å: Chain B: L.164, G.166, G.167, M.171, S.202, M.206, Y.209, Y.217, Y.219, A.222 Chain D: A.203, Y.207, E.216 Ligands: CDL.5 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.164, B:Y.209, B:Y.217, B:A.222, D:Y.207 Hydrogen bonds: B:Y.217, B:Y.219 PLX.7: 3 residues within 4Å: Chain B: W.184 Chain D: F.197, I.198 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.197, D:I.198 PLX.9: 17 residues within 4Å: Chain A: Y.207, F.210, E.216 Chain C: L.162, V.163, L.164, G.166, G.167, M.171, S.202, A.205, M.206, Y.209, Y.217, Y.219 Ligands: CDL.8, PLX.10 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:Y.207, A:F.210, C:L.162, C:L.164, C:A.205, C:Y.209, C:Y.217 Hydrogen bonds: C:Y.217, C:Y.219, C:Y.219 pi-Cation interactions: C:Y.219 PLX.10: 9 residues within 4Å: Chain C: Y.170, F.197, I.198, G.201, S.202 Chain D: W.183, W.184 Ligands: CDL.8, PLX.9 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.198, D:W.183 PLX.11: 5 residues within 4Å: Chain A: F.197, I.198 Chain C: W.183, W.184 Ligands: CDL.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.198 PLX.12: 15 residues within 4Å: Chain C: Y.207 Chain D: L.162, V.163, L.164, G.166, G.167, M.171, S.202, A.205, M.206, Y.209, Y.217, V.218, Y.219 Ligands: CDL.13 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:V.163, D:V.163, D:L.164, D:A.205, D:Y.209, D:Y.209, D:Y.219 Hydrogen bonds: D:Y.217, D:Y.219 pi-Cation interactions: D:Y.219 PLX.16: 14 residues within 4Å: Chain K: V.163, L.164, G.166, G.167, M.171, S.202, M.206, Y.209, Y.217, Y.219, Q.226 Chain L: F.210, E.216 Ligands: CDL.15 8 PLIP interactions: 7 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:V.163, K:L.164, K:Y.209, K:Y.219, L:F.210 Hydrogen bonds: K:Y.217, K:Y.219, K:Y.219 PLX.17: 3 residues within 4Å: Chain K: W.183, W.184 Ligands: CDL.18 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:W.183 PLX.19: 14 residues within 4Å: Chain L: L.164, G.166, G.167, M.171, S.202, M.206, Y.209, Y.217, Y.219, A.222 Chain N: A.203, Y.207, E.216 Ligands: CDL.18 7 PLIP interactions: 6 interactions with chain L, 1 interactions with chain N Hydrophobic interactions: L:L.164, L:Y.209, L:Y.217, L:A.222, N:Y.207 Hydrogen bonds: L:Y.217, L:Y.219 PLX.20: 3 residues within 4Å: Chain L: W.184 Chain N: F.197, I.198 2 PLIP interactions: 2 interactions with chain N Hydrophobic interactions: N:F.197, N:I.198 PLX.22: 17 residues within 4Å: Chain K: Y.207, F.210, E.216 Chain M: L.162, V.163, L.164, G.166, G.167, M.171, S.202, A.205, M.206, Y.209, Y.217, Y.219 Ligands: CDL.21, PLX.23 11 PLIP interactions: 2 interactions with chain K, 9 interactions with chain M Hydrophobic interactions: K:Y.207, K:F.210, M:L.162, M:L.164, M:A.205, M:Y.209, M:Y.217 Hydrogen bonds: M:Y.217, M:Y.219, M:Y.219 pi-Cation interactions: M:Y.219 PLX.23: 9 residues within 4Å: Chain M: Y.170, F.197, I.198, G.201, S.202 Chain N: W.183, W.184 Ligands: CDL.21, PLX.22 2 PLIP interactions: 1 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: N:W.183, M:I.198 PLX.24: 4 residues within 4Å: Chain K: F.197, I.198 Chain M: W.183, W.184 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:I.198 PLX.26: 15 residues within 4Å: Chain M: Y.207 Chain N: L.162, V.163, L.164, G.166, G.167, M.171, S.202, A.205, M.206, Y.209, Y.217, V.218, Y.219 Ligands: CDL.25 10 PLIP interactions: 10 interactions with chain N Hydrophobic interactions: N:V.163, N:V.163, N:L.164, N:A.205, N:Y.209, N:Y.209, N:Y.219 Hydrogen bonds: N:Y.217, N:Y.219 pi-Cation interactions: N:Y.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhuo, W. et al., Structure of intact human MCU supercomplex with the auxiliary MICU subunits. Protein Cell (2021)

Release Date

2020-09-09

Peptides

Calcium uniporter protein, mitochondrial: ABCDKLMN
Essential MCU regulator, mitochondrial: EFGHOPQR
Calcium uptake protein 1, mitochondrial: IS
Calcium uptake protein 2, mitochondrial: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

K
N

L
O

M
P

N
Q

E
E

F
F

G
G

H
H

O
R

P
S

Q
T

R
U

I
I

S
V

J
J

T
W

Membrane

We predict this structure to be a membrane protein.
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Calcium uniporter protein, mitochondrial

Essential MCU regulator, mitochondrial

Calcium uptake protein 1, mitochondrial

Calcium uptake protein 2, mitochondrial

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