6H8K

Crystal structure of a variant (Q133C in PSST) of Yarrowia lipolytica complex I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.361 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Locking loop movement in the ubiquinone pocket of complex I disengages the proton pumps.

Cabrera-Orefice, A.Yoga, E.G.Wirth, C.Siegmund, K.Zwicker, K.Guerrero-Castillo, S.Zickermann, V.Hunte, C.Brandt, U.

(2018) Nat Commun 9: 4500-4500


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 1
1
335Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND1
EC: 7.1.1.2
Find proteins for Q9B6E8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6E8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 2,NADH dehydrogenase subunit 2
2
434Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND2
EC: 7.1.1.2
Find proteins for Q9B6C8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6C8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 3
3
110Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND3
EC: 7.1.1.2
Find proteins for Q9B6C7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6C7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 4
4
470Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND4
EC: 7.1.1.2
Find proteins for Q9B6D6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6D6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 5
5
616Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND5
EC: 7.1.1.2
Find proteins for Q9B6D3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6D3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 6
6
184Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND6
EC: 7.1.1.2
Find proteins for Q9B6E9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6E9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
NUAM protein
A
634Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuam
EC: 1.6.99.3
Find proteins for Q9UUU3 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUU3
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
B
370Yarrowia lipolyticaMutation(s): 0 
Gene Names: nubm (NUO51)
EC: 1.6.99.3, 7.1.1.2
Find proteins for Q9UUU2 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUU2
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
NUCM protein
C
383Yarrowia lipolyticaMutation(s): 0 
Gene Names: nucm
EC: 1.6.99.3
Find proteins for Q9UUU1 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUU1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NUEM protein
E
195N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
NUGM protein
G
133Yarrowia lipolyticaMutation(s): 0 
Gene Names: nugm
EC: 1.6.99.3
Find proteins for Q9UUU0 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUU0
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
H
154N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
I
140Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuim
EC: 1.6.99.3
Find proteins for Q9UUT8 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUT8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
K
147Yarrowia lipolyticaMutation(s): 1 
Gene Names: nukm
EC: 1.6.99.3
Find proteins for Q9UUT7 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUT7
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 4L
L
79Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND4L
EC: 7.1.1.2
Find proteins for Q9B6D4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6D4
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
Z, r
17N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
Y, AF
40N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
U
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
X
57N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
W
54N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
V
63N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
T, m, AI
20N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
S, AJ, AL
19N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
R
50N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
Q
70N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
P
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
F, f, AC, AH, AM
18N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
O, l
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
M
51N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
D
30N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
J
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
N
15N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
a, i
26N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
b
22N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
c, g, AE, AK, AO
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
d, o, AB, AN
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
e, w, z
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
h
47N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
j
48N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
k, s
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
n, q
36N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
p
76N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
t
45N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
u
32N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
v, y
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
x, AG
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AA
58N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AD
39N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B, I, K
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
A, H
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
2, 4, 5, 6, a, A, AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, b, B, c, d, D, e, E, F, f, g, G, H, h, i, I, j, J, k, l, m, M, N, n, o, O, p, P, q, Q, r, R, S, s, t, T, u, U, v, V, w, W, x, X, y, Y, z, Z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.361 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 316.310α = 90.00
b = 316.310β = 90.00
c = 819.180γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
AutoPROCdata scaling
BUSTERrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
GermanyEXC 294 BIOSS
German Research FoundationGermanyZI552/4-1

Revision History 

  • Version 1.0: 2018-12-26
    Type: Initial release