› 7ar8

Electron Microscopy
3.53Å resolution

Cryo-EM structure of Arabidopsis thaliana complex-I (closed conformation)

Released:
DOI: 10.2210/pdb7ar8/pdb
PDB entry 7ar8 coloured by chain, front view.
PDB entry 7ar8 coloured by chain, side view.
PDB entry 7ar8 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
A ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Klusch N, Senkler J, Yildiz Ö, Kühlbrandt W, Braun HP
OpenAccess logo Plant Cell 33 2072-2091 (2021)
PMID: 33768254
Related structures: EMD-11876

Function and Biology Details

Reaction catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 47-mer (preferred)
PDBe Complex ID:
PDB-CPX-126459 (preferred)
Entry contents:
47 distinct polypeptide molecules
Macromolecules (47 distinct):
NADH-ubiquinone oxidoreductase chain 3 Chain: A
Molecule details ›
Chain: A
Length: 119 amino acids
Theoretical weight: 13.94 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P92533 (Residues: 1-119; Coverage: 100%)
Gene names: AtMg00990, NAD3, ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 218 amino acids
Theoretical weight: 24.07 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q42577 (Residues: 1-218; Coverage: 100%)
Gene names: At5g11770, T22P22_160
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 Chain: C
Molecule details ›
Chain: C
Length: 190 amino acids
Theoretical weight: 22.91 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q95748 (Residues: 1-190; Coverage: 100%)
Gene names: AtMg00070, NAD9
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 Chain: D
Molecule details ›
Chain: D
Length: 394 amino acids
Theoretical weight: 45.04 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P93306 (Residues: 1-394; Coverage: 100%)
Gene names: AtMg00510, NAD7
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: E
Molecule details ›
Chain: E
Length: 255 amino acids
Theoretical weight: 28.42 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: O22769 (Residues: 1-255; Coverage: 100%)
Gene names: At4g02580, T10P11.14
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: F
Molecule details ›
Chain: F
Length: 486 amino acids
Theoretical weight: 53.52 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FNN5 (Residues: 1-486; Coverage: 100%)
Gene names: At5g08530, MAH20.9
Sequence domains:
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial Chain: G
Molecule details ›
Chain: G
Length: 748 amino acids
Theoretical weight: 81.62 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FGI6 (Residues: 1-748; Coverage: 100%)
Gene names: At5g37510, EMB1467, MPA22.5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 1 Chain: H
Molecule details ›
Chain: H
Length: 325 amino acids
Theoretical weight: 36.02 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P92558 (Residues: 1-325; Coverage: 100%)
Gene names: At2g07785, At2g07786, AtMg00516/AtMg01120/AtMg01275, NAD1, ND1
Sequence domains: NADH dehydrogenase
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial Chain: I
Molecule details ›
Chain: I
Length: 222 amino acids
Theoretical weight: 25.54 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q42599 (Residues: 1-222; Coverage: 100%)
Gene names: At1g79010, YUP8H12R.37, YUP8H12R_21
Sequence domains: 4Fe-4S dicluster domain
NADH-ubiquinone oxidoreductase chain 6 Chain: J
Molecule details ›
Chain: J
Length: 205 amino acids
Theoretical weight: 23.69 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P60497 (Residues: 1-205; Coverage: 100%)
Gene names: AtMg00270, NAD6, ND6
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NADH-ubiquinone oxidoreductase chain 4L Chain: K
Molecule details ›
Chain: K
Length: 100 amino acids
Theoretical weight: 11.17 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q04614 (Residues: 1-100; Coverage: 100%)
Gene names: AtMg00650, NAD4L, ND4L
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
NADH-ubiquinone oxidoreductase chain 5 Chain: L
Molecule details ›
Chain: L
Length: 669 amino acids
Theoretical weight: 74.5 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P29388 (Residues: 1-669; Coverage: 100%)
Gene names: AtMg00060/AtMg00513/AtMg00665, NAD5, NAD5C, ND5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 4 Chain: M
Molecule details ›
Chain: M
Length: 495 amino acids
Theoretical weight: 56 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P93313 (Residues: 1-495; Coverage: 100%)
Gene names: AtMg00580, NAD4, ND4
Sequence domains: Proton-conducting membrane transporter
NADH-ubiquinone oxidoreductase chain 2 Chain: N
Molecule details ›
Chain: N
Length: 499 amino acids
Theoretical weight: 55.49 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: O05000 (Residues: 1-499; Coverage: 100%)
Gene names: AtMg00285/AtMg01320, NAD2, ND2
Sequence domains: Proton-conducting membrane transporter
F21O3.19 protein Chain: O
Molecule details ›
Chain: O
Length: 159 amino acids
Theoretical weight: 17.63 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SRR8 (Residues: 1-159; Coverage: 100%)
Gene names: At3g07480, F21O3.19
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: P
Molecule details ›
Chain: P
Length: 402 amino acids
Theoretical weight: 43.99 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SK66 (Residues: 1-402; Coverage: 100%)
Gene names: At2g20360, F11A3.9
Sequence domains: NAD dependent epimerase/dehydratase family
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 154 amino acids
Theoretical weight: 17.16 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FJW4 (Residues: 1-154; Coverage: 100%)
Gene names: At5g67590, FRO1, K9I9.16
Sequence domains: NADH dehydrogenase ubiquinone Fe-S protein 4
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: R
Molecule details ›
Chain: R
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9M9M6 (Residues: 1-110; Coverage: 100%)
Gene names: At3g03070, T17B22_24
Sequence domains: Zinc-finger domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: S
Molecule details ›
Chain: S
Length: 97 amino acids
Theoretical weight: 10.87 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FIJ2 (Residues: 1-97; Coverage: 100%)
Gene names: At5g47890, MCA23_23
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Acyl carrier protein 1, mitochondrial Chain: T
Molecule details ›
Chain: T
Length: 122 amino acids
Theoretical weight: 13.74 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P53665 (Residues: 1-122; Coverage: 100%)
Gene names: At2g44620, F16B22.11, MTACP1
Sequence domains: Phosphopantetheine attachment site
Acyl carrier protein 2, mitochondrial Chain: U
Molecule details ›
Chain: U
Length: 126 amino acids
Theoretical weight: 14.18 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: O80800 (Residues: 1-126; Coverage: 100%)
Gene names: At1g65290, MTACP2, T8F5.6
Sequence domains: Phosphopantetheine attachment site
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial Chain: V
Molecule details ›
Chain: V
Length: 169 amino acids
Theoretical weight: 19.2 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FLX7 (Residues: 1-169; Coverage: 100%)
Gene names: At5g52840, MXC20.6
Sequence domains: ETC complex I subunit conserved region
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: W
Molecule details ›
Chain: W
Length: 133 amino acids
Theoretical weight: 15.1 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9LHI0 (Residues: 1-133; Coverage: 100%)
Gene names: At3g12260, F28J15.12, MQC3.9
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B Chain: X
Molecule details ›
Chain: X
Length: 106 amino acids
Theoretical weight: 11.99 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q8LGE7 (Residues: 1-106; Coverage: 100%)
Gene names: At5g18800, F17K4.50
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A Chain: Z
Molecule details ›
Chain: Z
Length: 143 amino acids
Theoretical weight: 16.15 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q8RWA7 (Residues: 1-143; Coverage: 100%)
Gene names: At1g04630, MEE4, T1G11.12
Sequence domains: GRIM-19 protein
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: a
Molecule details ›
Chain: a
Length: 65 amino acids
Theoretical weight: 7.35 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9C9Z5 (Residues: 1-65; Coverage: 100%)
Gene names: At3g08610, F17O14.8
Sequence domains: NADH-ubiquinone oxidoreductase MWFE subunit
At2g46540/F11C10.23 Chain: b
Molecule details ›
Chain: b
Length: 65 amino acids
Theoretical weight: 6.81 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9ZPY5 (Residues: 1-65; Coverage: 100%)
Gene names: At2g46540, F13A10.7, F13A10_7
Transmembrane protein Chain: c
Molecule details ›
Chain: c
Length: 88 amino acids
Theoretical weight: 9.88 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q8VZT9 (Residues: 1-88; Coverage: 100%)
Gene name: At4g00585
Excitatory amino acid transporter Chain: d
Molecule details ›
Chain: d
Length: 81 amino acids
Theoretical weight: 9.22 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q94AL6 (Residues: 1-81; Coverage: 100%)
Gene names: At4g20150, F1C12.70, F1C12_70
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B Chain: e
Molecule details ›
Chain: e
Length: 83 amino acids
Theoretical weight: 9.91 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9LZI6 (Residues: 1-83; Coverage: 100%)
Gene names: At3g62790, F26K9_220
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
NADH-ubiquinone oxidoreductase 21kDa subunit N-terminal domain-containing protein Chain: f
Molecule details ›
Chain: f
Length: 106 amino acids
Theoretical weight: 11.36 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q84W12 (Residues: 1-106; Coverage: 100%)
Gene names: At4g16450, DL4250W, FCAALL.388
Sequence domains: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein Chain: g
Molecule details ›
Chain: g
Length: 114 amino acids
Theoretical weight: 12.65 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SLC8 (Residues: 1-114; Coverage: 100%)
Gene names: At2g42310, MHK10.3, MHK10_3
F1N21.17 Chain: i
Molecule details ›
Chain: i
Length: 98 amino acids
Theoretical weight: 11.81 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FYF8 (Residues: 1-98; Coverage: 100%)
Gene names: At1g67350, F1N21.17
Sequence domains: NADH-ubiquinone oxidoreductase 11 kDa subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 Chain: j
Molecule details ›
Chain: j
Length: 69 amino acids
Theoretical weight: 7.58 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q8LDK3 (Residues: 1-69; Coverage: 100%)
Gene names: At1g76200, T23E18.30
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A Chain: k
Molecule details ›
Chain: k
Length: 72 amino acids
Theoretical weight: 8.06 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: O64725 (Residues: 1-72; Coverage: 100%)
Gene names: At2g02510, T8K22.19
Sequence domains: NADH-ubiquinone oxidoreductase B12 subunit family
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: l
Molecule details ›
Chain: l
Length: 125 amino acids
Theoretical weight: 13.23 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FGK0 (Residues: 1-125; Coverage: 100%)
Gene names: At5g47570, MNJ7.16
AT2G31490 protein Chain: m
Molecule details ›
Chain: m
Length: 71 amino acids
Theoretical weight: 8.31 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SIQ8 (Residues: 1-71; Coverage: 100%)
Gene names: At2g31490, T28P16.2, T28P16_2
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: n
Molecule details ›
Chain: n
Length: 117 amino acids
Theoretical weight: 13.64 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q945M1 (Residues: 1-117; Coverage: 100%)
Gene names: At4g34700, CIB22, T4L20_280
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: o
Molecule details ›
Chain: o
Length: 103 amino acids
Theoretical weight: 11.76 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SKC9 (Residues: 1-103; Coverage: 100%)
Gene names: At2g02050, F14H20.12
Sequence domains: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B Chain: p
Molecule details ›
Chain: p
Length: 106 amino acids
Theoretical weight: 12.46 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q94C12 (Residues: 1-106; Coverage: 100%)
Gene names: At3g18410, MYF24_12
Sequence domains: NADH-ubiquinone oxidoreductase subunit 10
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chain: q
Molecule details ›
Chain: q
Length: 159 amino acids
Theoretical weight: 18.35 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9M9M9 (Residues: 1-159; Coverage: 100%)
Gene names: At3g03100, T17B22.21
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12
Furry Chain: r
Molecule details ›
Chain: r
Length: 131 amino acids
Theoretical weight: 15.06 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SD78 (Residues: 1-131; Coverage: 100%)
Gene names: At5g08060, At5g08060/F13G24_260, F13G24.260, T22D6.4
unknown Chain: u
Molecule details ›
Chain: u
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Arabidopsis thaliana
Uncharacterized protein At2g27730, mitochondrial Chain: v
Molecule details ›
Chain: v
Length: 113 amino acids
Theoretical weight: 11.97 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9ZUX4 (Residues: 1-113; Coverage: 100%)
Gene names: At2g27730, F15K20.17
Gamma carbonic anhydrase-like 2, mitochondrial Chain: x
Molecule details ›
Chain: x
Length: 256 amino acids
Theoretical weight: 27.99 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SMN1 (Residues: 1-256; Coverage: 100%)
Gene names: At3g48680, GAMMACAL2, T8P19.190
Gamma carbonic anhydrase 2, mitochondrial Chain: y
Molecule details ›
Chain: y
Length: 278 amino acids
Theoretical weight: 30.1 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9C6B3 (Residues: 1-278; Coverage: 100%)
Gene names: APFI, At1g47260, F8G22.2, GAMMACA2
Sequence domains: Bacterial transferase hexapeptide (six repeats)
Gamma carbonic anhydrase 1, mitochondrial Chain: z
Molecule details ›
Chain: z
Length: 275 amino acids
Theoretical weight: 30.01 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9FWR5 (Residues: 1-275; Coverage: 100%)
Gene names: At1g19580, F14P1.8, F18O14.34, GAMMACA1

Ligands and Environments

14 bound ligands:
Ligand SF4 6 x SF4
Ligand FES 2 x FES
Ligand FMN 1 x FMN
Ligand UQ9 1 x UQ9
Ligand PTY 3 x PTY
Ligand PC7 2 x PC7
Ligand PGT 1 x PGT
Ligand FE 1 x FE
Ligand NDP 1 x NDP
Ligand ZN 2 x ZN
Ligand 8Q1 2 x 8Q1
Ligand LMN 1 x LMN
Ligand PSF 1 x PSF
Ligand T7X 1 x T7X
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.53Å
Relevant EMDB volumes: EMD-11876

Quick links

Citations

11 review citations

Structure of respiratory complex I - An emerging blueprint for the mechanism.
Kampjut et al. (2022)
10 more

2 mentions without citation

From the 'black box' to 'domino effect' mechanism: what have we learned from the structures of respiratory complex I.
Sazanov LA. (2023)
1 more