SMTL ID : 6k7x.1

Human MCU-EMRE complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-mer

Ligands

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 19 residues within 4Å: Chain A: M.204, A.205, A.208, Y.209, M.212, T.213, R.225, Q.226, L.229, F.230, K.233 Chain D: F.175 Chain F: K.15, L.20, V.23, F.24, L.31 Ligands: PLX.2, PLX.15 10 PLIP interactions: 4 interactions with chain A, 5 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: A:A.205, A:A.208, F:L.20, F:L.20, F:V.23, F:F.24, F:L.31, D:F.175 Salt bridges: A:R.225, A:K.233 CDL.7: 21 residues within 4Å: Chain A: F.175 Chain B: K.155, K.158, R.159, Y.170, I.198, M.204, A.205, Y.209, M.212, T.213, R.225, Q.226, L.229, K.233 Chain G: K.15, L.20, V.23, F.24, L.31 Ligands: PLX.8 15 PLIP interactions: 8 interactions with chain G, 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: G:L.20, G:L.20, G:V.23, G:F.24, G:F.24, G:L.31, B:Y.170, B:I.198, B:A.205, A:F.175 Hydrogen bonds: G:K.15 Salt bridges: G:K.15, B:R.225, B:K.233, B:K.233 CDL.10: 18 residues within 4Å: Chain B: F.175, A.179 Chain C: V.163, Y.170, A.205, A.208, Y.209, M.212, T.213, R.225, Q.226, L.229, F.230, K.233 Chain H: K.15, L.20, F.24 Ligands: PLX.11 17 PLIP interactions: 10 interactions with chain C, 5 interactions with chain H, 2 interactions with chain B Hydrophobic interactions: C:V.163, C:V.163, C:Y.170, C:A.205, C:A.208, C:F.230, H:L.20, H:L.20, H:F.24, H:F.24, B:F.175, B:A.179 Hydrogen bonds: C:Q.226, C:Q.226 Salt bridges: C:R.225, C:K.233, H:K.15 CDL.13: 16 residues within 4Å: Chain D: M.204, A.205, Y.209, M.212, T.213, R.225, Q.226, F.230, K.233 Chain E: K.15, L.20, L.21, F.24, I.28 Ligands: PLX.12, PLX.14 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.20, E:L.20, E:F.24 Hydrogen bonds: E:K.15, D:Q.226 Salt bridges: E:K.15, E:K.15, D:R.225, D:K.233 CDL.18: 19 residues within 4Å: Chain I: M.204, A.205, A.208, Y.209, M.212, T.213, R.225, Q.226, L.229, F.230, K.233 Chain L: F.175 Chain N: K.15, L.20, V.23, F.24, L.31 Ligands: PLX.19, PLX.30 10 PLIP interactions: 5 interactions with chain N, 1 interactions with chain L, 4 interactions with chain I Hydrophobic interactions: N:L.20, N:L.20, N:V.23, N:F.24, N:L.31, L:F.175, I:A.205, I:A.208 Salt bridges: I:R.225, I:K.233 CDL.22: 22 residues within 4Å: Chain I: F.175 Chain J: K.155, K.158, R.159, Y.170, I.198, M.204, A.205, Y.209, M.212, T.213, R.225, Q.226, L.229, K.233 Chain O: K.15, L.20, V.23, F.24, L.31 Ligands: PLX.20, PLX.23 15 PLIP interactions: 8 interactions with chain O, 1 interactions with chain I, 6 interactions with chain J Hydrophobic interactions: O:L.20, O:L.20, O:V.23, O:F.24, O:F.24, O:L.31, I:F.175, J:Y.170, J:I.198, J:A.205 Hydrogen bonds: O:K.15 Salt bridges: O:K.15, J:R.225, J:K.233, J:K.233 CDL.25: 18 residues within 4Å: Chain J: F.175, A.179 Chain K: V.163, Y.170, A.205, A.208, Y.209, M.212, T.213, R.225, Q.226, L.229, F.230, K.233 Chain P: K.15, L.20, F.24 Ligands: PLX.26 17 PLIP interactions: 10 interactions with chain K, 2 interactions with chain J, 5 interactions with chain P Hydrophobic interactions: K:V.163, K:V.163, K:Y.170, K:A.205, K:A.208, K:F.230, J:F.175, J:A.179, P:L.20, P:L.20, P:F.24, P:F.24 Hydrogen bonds: K:Q.226, K:Q.226 Salt bridges: K:R.225, K:K.233, P:K.15 CDL.28: 16 residues within 4Å: Chain L: M.204, A.205, Y.209, M.212, T.213, R.225, Q.226, F.230, K.233 Chain M: K.15, L.20, L.21, F.24, I.28 Ligands: PLX.27, PLX.29 10 PLIP interactions: 7 interactions with chain M, 3 interactions with chain L Hydrophobic interactions: M:L.20, M:L.20, M:L.21, M:F.24 Hydrogen bonds: M:K.15, L:Q.226 Salt bridges: M:K.15, M:K.15, L:R.225, L:K.233

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.2: 16 residues within 4Å: Chain A: L.162, V.163, G.166, G.167, M.171, S.202, M.206, Y.209, Y.217, Y.219, A.222 Chain B: A.203, Y.207, E.216 Ligands: CDL.1, PLX.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.162, A:V.163, A:Y.209, A:Y.217, A:A.222 Hydrogen bonds: A:Y.217, A:Y.219 PLX.3: 6 residues within 4Å: Chain A: W.183, W.184 Chain B: V.194, G.201 Chain H: F.51 Ligands: PLX.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:V.194, H:F.51 PLX.8: 18 residues within 4Å: Chain B: R.159, V.163, L.164, G.166, G.167, Y.170, M.171, S.202, A.205, M.206, Y.209, Y.217, V.218, Y.219, Q.226 Chain C: A.203 Ligands: PLX.3, CDL.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:R.159, B:V.163, B:L.164, B:A.205, B:Y.209, B:Y.217, B:Y.217, B:Y.219 Hydrogen bonds: B:Y.170, B:Y.170, B:S.202, B:Y.217 pi-Cation interactions: B:Y.219 PLX.9: 6 residues within 4Å: Chain B: W.183, W.184 Chain C: Y.170, F.197, G.201, S.202 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.183 PLX.11: 14 residues within 4Å: Chain C: V.163, L.164, G.166, G.167, M.171, S.202, M.206, Y.217, Y.219, A.222 Chain D: A.203, Y.207, E.216 Ligands: CDL.10 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.207, C:L.164 Hydrogen bonds: C:Y.217, C:Y.219 PLX.12: 5 residues within 4Å: Chain C: F.175, W.183, W.184 Chain D: Y.170 Ligands: CDL.13 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.175, C:W.183, C:W.183 PLX.14: 14 residues within 4Å: Chain A: E.216 Chain D: L.162, V.163, L.164, G.166, G.167, M.171, S.202, M.206, Y.209, Y.217, Y.219, Q.226 Ligands: CDL.13 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.162, D:V.163, D:L.164, D:Y.209, D:Y.217 Hydrogen bonds: D:Y.170, D:Y.170, D:Y.217, D:Y.219 PLX.15: 5 residues within 4Å: Chain A: G.201 Chain D: W.183, W.184 Ligands: CDL.1, PLX.2 No protein-ligand interaction detected (PLIP) PLX.19: 16 residues within 4Å: Chain I: L.162, V.163, G.166, G.167, M.171, S.202, M.206, Y.209, Y.217, Y.219, A.222 Chain J: A.203, Y.207, E.216 Ligands: CDL.18, PLX.30 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:L.162, I:V.163, I:Y.209, I:Y.217, I:A.222 Hydrogen bonds: I:Y.217, I:Y.219 PLX.20: 7 residues within 4Å: Chain I: W.183, W.184 Chain J: V.194, G.201 Chain P: F.51 Ligands: CDL.22, PLX.23 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain P Hydrophobic interactions: J:V.194, P:F.51 PLX.23: 18 residues within 4Å: Chain J: R.159, V.163, L.164, G.166, G.167, Y.170, M.171, S.202, A.205, M.206, Y.209, Y.217, V.218, Y.219, Q.226 Chain K: A.203 Ligands: PLX.20, CDL.22 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:R.159, J:V.163, J:L.164, J:A.205, J:Y.209, J:Y.217, J:Y.217, J:Y.219 Hydrogen bonds: J:Y.170, J:Y.170, J:S.202, J:Y.217 pi-Cation interactions: J:Y.219 PLX.24: 6 residues within 4Å: Chain J: W.183, W.184 Chain K: Y.170, F.197, G.201, S.202 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:W.183 PLX.26: 14 residues within 4Å: Chain K: V.163, L.164, G.166, G.167, M.171, S.202, M.206, Y.217, Y.219, A.222 Chain L: A.203, Y.207, E.216 Ligands: CDL.25 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:L.164, L:Y.207 Hydrogen bonds: K:Y.217, K:Y.219 PLX.27: 5 residues within 4Å: Chain K: F.175, W.183, W.184 Chain L: Y.170 Ligands: CDL.28 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:F.175, K:W.183, K:W.183 PLX.29: 14 residues within 4Å: Chain I: E.216 Chain L: L.162, V.163, L.164, G.166, G.167, M.171, S.202, M.206, Y.209, Y.217, Y.219, Q.226 Ligands: CDL.28 9 PLIP interactions: 9 interactions with chain L Hydrophobic interactions: L:L.162, L:V.163, L:L.164, L:Y.209, L:Y.217 Hydrogen bonds: L:Y.170, L:Y.170, L:Y.217, L:Y.219 PLX.30: 5 residues within 4Å: Chain I: G.201 Chain L: W.183, W.184 Ligands: CDL.18, PLX.19 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 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, 1 interactions with chain A, 2 interactions with chain D, 1 interactions with chain C Metal complexes: B:E.192, A:E.192, D:E.192, D:E.192, C:E.192 CA.5: 2 residues within 4Å: Chain B: D.189 Chain C: D.189 No protein-ligand interaction detected (PLIP) CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.16: 4 residues within 4Å: Chain I: E.192 Chain J: E.192 Chain K: E.192 Chain L: E.192 5 PLIP interactions: 1 interactions with chain J, 2 interactions with chain L, 1 interactions with chain K, 1 interactions with chain I Metal complexes: J:E.192, L:E.192, L:E.192, K:E.192, I:E.192 CA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.21: 2 residues within 4Å: Chain J: D.189 Chain K: D.189 No protein-ligand interaction detected (PLIP)

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: ABCDIJKL
Essential MCU regulator, mitochondrial: EFGHMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
D

I
K

J
L

K
M

L
N

E
H

F
E

G
F

H
G

M
O

N
P

O
Q

P
R

Calcium uniporter protein, mitochondrial

Essential MCU regulator, mitochondrial

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