SMTL ID : 5luf.1

Cryo-EM of bovine respirasome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 24 residues within 4Å: Chain C: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, R.80, H.83, A.84, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:Q.44, C:I.45, C:L.49, C:A.52, C:Y.55, C:F.90, C:T.126, C:A.127, C:L.133, C:F.179, C:F.183, C:F.183, C:P.186 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.182 HEM.2: 21 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, L.94, H.97, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:T.112, C:W.113, C:V.117, C:L.119, C:L.119, C:L.120, C:L.197, C:L.200, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:S.106, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.4: 24 residues within 4Å: Chain N: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 17 PLIP interactions: 17 interactions with chain N, Hydrophobic interactions: N:L.41, N:Q.44, N:I.45, N:L.51, N:A.52, N:Y.55, N:F.90, N:T.126, N:A.127, N:L.133, N:F.179, N:F.183, N:F.183, N:P.186 Salt bridges: N:R.80, N:R.80 Metal complexes: N:H.182 HEM.5: 23 residues within 4Å: Chain N: W.31, G.34, S.35, L.37, G.38, F.90, L.94, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 24 PLIP interactions: 24 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:L.37, N:F.90, N:V.98, N:T.112, N:W.113, N:V.117, N:L.119, N:L.119, N:L.120, N:L.197, N:L.200, N:L.200 Hydrogen bonds: N:G.34, N:S.106, N:S.205, N:S.205, N:N.206 Salt bridges: N:H.97, N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196

2 x HEC: HEME C(Covalent)

HEC.3: 20 residues within 4Å: Chain D: V.36, C.37, S.39, C.40, H.41, N.105, A.108, L.113, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, I.164, V.186, L.190 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:N.105, D:A.108, D:L.113, D:L.113, D:Y.126, D:V.127, D:L.130, D:I.158, D:I.158, D:I.164, D:V.186, D:L.190 Hydrogen bonds: D:Y.126, D:G.159 Salt bridges: D:R.120 Metal complexes: D:H.41 HEC.6: 18 residues within 4Å: Chain O: V.36, C.37, C.40, H.41, N.105, A.108, L.113, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, I.164, L.190 15 PLIP interactions: 15 interactions with chain O, Hydrophobic interactions: O:N.105, O:A.108, O:L.113, O:L.113, O:Y.126, O:V.127, O:L.130, O:L.131, O:I.158, O:I.164, O:L.190 Hydrogen bonds: O:Y.126, O:G.159 Salt bridges: O:R.120 Metal complexes: O:H.41

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.7: 9 residues within 4Å: Chain P: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, S.163 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.139, P:H.141, P:C.158, P:H.161 FES.16: 10 residues within 4Å: Chain d: C.84, X.86, X.88, C.89, C.125, X.126, X.127, X.128, C.129 Chain e: X.72 4 PLIP interactions: 4 interactions with chain d, Metal complexes: d:C.84, d:C.89, d:C.125, d:C.129 FES.20: 9 residues within 4Å: Chain f: X.33, C.34, X.42, X.44, C.45, X.46, X.47, C.48, C.62 4 PLIP interactions: 4 interactions with chain f, Metal complexes: f:C.34, f:C.45, f:C.48, f:C.62

3 x CU: COPPER (II) ION(Non-covalent)

CU.8: 3 residues within 4Å: Chain W: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:H.240, W:H.290, W:H.291 CU.12: 6 residues within 4Å: Chain X: H.161, C.196, E.198, C.200, M.207 Ligands: CU.13 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:H.161, X:C.196, X:C.200 CU.13: 5 residues within 4Å: Chain X: C.196, E.198, C.200, H.204 Ligands: CU.12 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.196, X:E.198, X:C.200, X:H.204

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain W: H.368, D.369 Chain X: E.198 3 PLIP interactions: 1 interactions with chain X, 2 interactions with chain W Metal complexes: X:E.198, W:H.368, W:D.369

2 x HEA: HEME-A(Covalent)(Non-covalent)

HEA.10: 34 residues within 4Å: Chain W: A.24, G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, I.73, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, M.390, F.393, T.424, F.425, Q.428, R.438, R.439, Y.440, M.468 32 PLIP interactions: 32 interactions with chain W, Hydrophobic interactions: W:A.24, W:I.37, W:V.58, W:V.58, W:A.62, W:M.65, W:I.66, W:V.70, W:I.73, W:V.374, W:F.377, W:L.381, W:V.386, W:V.386, W:F.393, W:F.393, W:T.424, W:F.425 Hydrogen bonds: W:R.38, W:Y.54, W:W.126, W:Y.371, W:S.382, W:Q.428, W:R.439, W:Y.440 Salt bridges: W:R.438, W:R.439 pi-Stacking: W:F.377, W:F.425 Metal complexes: W:H.61, W:H.378 HEA.11: 29 residues within 4Å: Chain W: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, A.313, T.316, G.317, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain X: I.34, P.69 22 PLIP interactions: 20 interactions with chain W, 2 interactions with chain X, Hydrophobic interactions: W:W.236, W:V.243, W:Y.244, W:I.247, W:T.309, W:A.313, W:F.348, W:I.356, W:V.373, W:F.377, W:F.377, W:V.380, W:L.381, X:I.34, X:P.69 Hydrogen bonds: W:W.126, W:Y.244 Salt bridges: W:H.291, W:H.368, W:R.438 pi-Cation interactions: W:H.240 Metal complexes: W:H.376

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 5 residues within 4Å: Chain 1: C.60, C.62, C.82, S.84, C.85 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.60, 1:C.62, 1:C.82, 1:C.85

6 x SF4: IRON/SULFUR CLUSTER(Covalent)(Non-covalent)

SF4.15: 9 residues within 4Å: Chain a: X.27, C.28, C.29, X.64, X.91, X.92, C.93, C.123, X.124 4 PLIP interactions: 4 interactions with chain a, Metal complexes: a:C.28, a:C.29, a:C.93, a:C.123 SF4.17: 9 residues within 4Å: Chain e: X.328, C.329, X.330, X.331, C.332, C.335, X.374, C.375, X.378 4 PLIP interactions: 4 interactions with chain e, Metal complexes: e:C.329, e:C.332, e:C.335, e:C.375 SF4.18: 8 residues within 4Å: Chain f: H.94, X.97, C.98, C.101, X.103, C.107, X.110, X.199 4 PLIP interactions: 4 interactions with chain f, Metal complexes: f:H.94, f:C.98, f:C.101, f:C.107 SF4.19: 8 residues within 4Å: Chain f: C.147, X.148, X.149, C.150, X.152, C.153, C.197, X.201 4 PLIP interactions: 4 interactions with chain f, Metal complexes: f:C.147, f:C.150, f:C.153, f:C.197 SF4.21: 9 residues within 4Å: Chain h: C.73, X.75, C.102, X.103, X.104, C.105, X.106, X.107, C.108 4 PLIP interactions: 4 interactions with chain h, Metal complexes: h:C.73, h:C.102, h:C.105, h:C.108 SF4.22: 9 residues within 4Å: Chain h: C.63, X.64, X.65, C.66, X.67, X.68, C.69, C.112, X.116 4 PLIP interactions: 4 interactions with chain h, Metal complexes: h:C.63, h:C.66, h:C.69, h:C.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sousa, J.S. et al., Functional asymmetry and electron flow in the bovine respirasome. Elife (2016)

Release Date

2016-11-30

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AL
Cytochrome b-c1 complex subunit 2, mitochondrial: BM
Cytochrome b: CN
Cytochrome c1, heme protein, mitochondrial: DO
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EP
Cytochrome b-c1 complex subunit 7: FQ
Cytochrome b-c1 complex subunit 8: GR
Cytochrome b-c1 complex subunit 6, mitochondrial: HS
Cytochrome b-c1 complex subunit Rieske, mitochondrial: IT
Cytochrome b-c1 complex subunit 9: JU
Cytochrome b-c1 complex subunit 10: KV
Cytochrome c oxidase subunit 1: W
Cytochrome c oxidase subunit 2: X
Cytochrome c oxidase subunit 3: Y
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial: Z
Cytochrome c oxidase subunit 5A, mitochondrial: 0
Cytochrome c oxidase subunit 5B, mitochondrial: 1
Cytochrome c oxidase subunit 6A2, mitochondrial: 2
Cytochrome c oxidase subunit 6B1: 3
Cytochrome c oxidase subunit 6C: 4
Cytochrome c oxidase subunit 7A1, mitochondrial: 5
Cytochrome c oxidase subunit 7B, mitochondrial: 6
Cytochrome c oxidase subunit 7C, mitochondrial: 7
Cytochrome c oxidase subunit 8B, mitochondrial: 8
complex I: 9
complex I: a
complex I: b
complex I: c
complex I: d
complex I: e
complex I: f
complex I: g
complex I: h
complex I: i
complex I: j
complex I: k
complex I: l
complex I: m
complex I: n
complex I: o
complex I: p
complex I: q
complex I: r
complex I: s
complex I: t
complex I: u
complex I: v
complex I: w
complex I: x
complex I: y
complex I: z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
c

L
l

B
m

M
n

C
b

N
o

D
d

O
p

E
e

P
q

F
f

Q
r

G
g

R
s

H
h

S
t

I
i

T
u

J
j

U
v

K
k

V
w

W
x

X
y

Y
z

Z
1

0
2

1
3

2
4

3
5

4
6

5
7

6
8

7
9

8
0

9
A

a
B

b
C

c
D

d
E

e
F

f
G

g
H

h
I

i
J

j
K

k
L

l
M

m
N

n
O

o
P

p
Q

q
R

r
S

s
T

t
V

u
W

v
X

w
Y

x
a

y
U

z
Z

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 9

Cytochrome b-c1 complex subunit 10

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 5B, mitochondrial

Cytochrome c oxidase subunit 6A2, mitochondrial

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A1, mitochondrial

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B, mitochondrial

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

complex I

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