ISDA

Deposition Date 2020-10-23

Release Date 2021-12-08

Last Version Date 2025-07-02

Entry Detail

PDB ID:

7ARD

Keywords:

ELECTRON TRANSPORT

Title:

Cryo-EM structure of Polytomella Complex-I (complete composition)

Biological Source:

Source Organism:

Polytomella sp. Pringsheim 198.80 (Taxon ID: 37502)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.11 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:ND3
Chain IDs:A
Chain Length:154
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:PSST
Chain IDs:B
Chain Length:164
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:ND9
Chain IDs:C
Chain Length:217
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:ND7
Chain IDs:D
Chain Length:83
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:24 kDa
Chain IDs:E
Chain Length:75
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:51 kDa
Chain IDs:F
Chain Length:121
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:75 kDa
Chain IDs:G
Chain Length:720
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:ND1
Chain IDs:H
Chain Length:81
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:TYKY
Chain IDs:I
Chain Length:128
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:ND6
Chain IDs:J
Chain Length:87
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:ND4L
Chain IDs:K
Chain Length:55
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:ND5
Chain IDs:L
Chain Length:151
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:ND4
Chain IDs:M
Chain Length:138
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:ND2
Chain IDs:N
Chain Length:121
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:C1-FDX
Chain IDs:O
Chain Length:85
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:39 kDa
Chain IDs:P
Chain Length:156
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:18 kDa
Chain IDs:Q
Chain Length:185
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:13 kDa
Chain IDs:R
Chain Length:121
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B8
Chain IDs:S
Chain Length:98
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:SDAP1
Chain IDs:T
Chain Length:134
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:SDAP2
Chain IDs:U
Chain Length:122
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B13
Chain IDs:V
Chain Length:159
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B14
Chain IDs:W
Chain Length:41
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:PGIV
Chain IDs:X
Chain Length:280
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B14.7
Chain IDs:Y
Chain Length:206
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B16.6
Chain IDs:Z
Chain Length:142
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:MWFE
Chain IDs:AA (auth: a)
Chain Length:154
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B9
Chain IDs:BA (auth: b)
Chain Length:164
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:KFYI
Chain IDs:CA (auth: c)
Chain Length:217
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B14.5b
Chain IDs:DA (auth: d)
Chain Length:83
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:15 kDa
Chain IDs:EA (auth: e)
Chain Length:75
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:MNLL
Chain IDs:FA (auth: f)
Chain Length:121
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:ESSS
Chain IDs:GA (auth: g)
Chain Length:720
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:NUOP4
Chain IDs:HA (auth: h)
Chain Length:81
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:NUOP5
Chain IDs:IA (auth: i)
Chain Length:128
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:AGGG
Chain IDs:JA (auth: j)
Chain Length:87
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B12
Chain IDs:KA (auth: k)
Chain Length:55
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:ASHI
Chain IDs:LA (auth: l)
Chain Length:151
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B15
Chain IDs:MA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Complex I-B22
Gene (Uniprot):nuob22
Chain IDs:NA (auth: n)
Chain Length:121
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

UniProt ID:A0A024FSS5 Pfam ID:PF05347

Polymer Type:polypeptide(L)
Molecule:B18
Chain IDs:OA (auth: o)
Chain Length:85
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:PDSW
Chain IDs:PA (auth: p)
Chain Length:156
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B17.2
Chain IDs:QA (auth: q)
Chain Length:185
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:B14.5a
Chain IDs:RA (auth: r)
Chain Length:121
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:NUOP7
Chain IDs:SA (auth: s)
Chain Length:98
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:NUOP8
Chain IDs:TA (auth: t)
Chain Length:134
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:unknown
Chain IDs:UA (auth: u)
Chain Length:122
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:unknown
Chain IDs:VA (auth: w)
Chain Length:41
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:CAL
Chain IDs:WA (auth: x)
Chain Length:280
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:CA2
Chain IDs:XA (auth: y)
Chain Length:206
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Polymer Type:polypeptide(L)
Molecule:CA3
Chain IDs:YA (auth: z)
Chain Length:142
Number of Molecules:1
Biological Source:Polytomella sp. Pringsheim 198.80

Ligand Molecules

8Q1

CDL

FES

FMN

NDP

PC7

PTY

SF4

Primary Citation

A ferredoxin bridge connects the two arms of plant mitochondrial complex I.

Klusch, N, Senkler, J, Yildiz, O, Kuhlbrandt, W, Braun, H.P.Show

Plant Cell 33 2072 2091 (2021)

PMID: 33768254 DOI: 10.1093/plcell/koab092

Abstact

Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.

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Protein

Chemical

Disease

Primary Citation of related structures