[English] 日本語
Yorodumi
- PDB-7aqw: Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane tip) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7aqw
TitleCryo-EM structure of Arabidopsis thaliana Complex-I (membrane tip)
Components
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 6
  • (NADH-ubiquinone oxidoreductase chain ...) x 2
  • Acyl carrier protein 1, mitochondrial
  • B15 -- 1 beta subcomplex subunit 4
  • ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
  • P1
  • Transmembrane protein
KeywordsELECTRON TRANSPORT / Complex-I
Function / homology
Function and homology information


photorespiration / plant-type vacuole / respiratory chain complex I / plastid / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity ...photorespiration / plant-type vacuole / respiratory chain complex I / plastid / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / mitochondrial membrane / mitochondrial intermembrane space / fatty acid biosynthetic process / mitochondrial inner membrane / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 ...Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Chem-8Q1 / Chem-PC7 / PHOSPHATIDYLETHANOLAMINE / (thale cress) hypothetical protein / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A / Acyl carrier protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 ...Chem-8Q1 / Chem-PC7 / PHOSPHATIDYLETHANOLAMINE / (thale cress) hypothetical protein / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A / Acyl carrier protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / Transmembrane protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsKlusch, N. / Kuehlbrandt, W. / Yildiz, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Plant Cell / Year: 2021
Title: A ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Authors: Niklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: 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 ...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.
History
DepositionOct 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11874
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: NADH-ubiquinone oxidoreductase chain 5
M: NADH-ubiquinone oxidoreductase chain 4
T: Acyl carrier protein 1, mitochondrial
c: Transmembrane protein
g: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
i: P1
j: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
l: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
m: B15 -- 1 beta subcomplex subunit 4
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,63616
Polymers253,59813
Non-polymers2,0383
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
NADH-ubiquinone oxidoreductase chain ... , 2 types, 2 molecules LM

#1: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 74497.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: B5TM94, NADH:ubiquinone reductase (H+-translocating)
#2: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 55995.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: B5TM93, NADH:ubiquinone reductase (H+-translocating)

-
Protein , 5 types, 5 molecules Tcgim

#3: Protein Acyl carrier protein 1, mitochondrial / MtACP-1 / ACP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 13735.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P53665
#4: Protein Transmembrane protein /


Mass: 9876.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VZT9
#5: Protein ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein


Mass: 12648.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SLC8
#6: Protein P1


Mass: 11808.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178W1I8
#10: Protein B15 -- 1 beta subcomplex subunit 4


Mass: 8305.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178VZI4

-
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 6 types, 6 molecules jklnop

#7: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2


Mass: 7582.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LDK3
#8: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A


Mass: 8064.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O64725
#9: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial


Mass: 13225.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FGK0
#11: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / B22 subunit of eukaryotic mitochondrial complex I / Complex I-B22 / CI-B22 / NADH-ubiquinone ...B22 subunit of eukaryotic mitochondrial complex I / Complex I-B22 / CI-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 13638.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q945M1
#12: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 11757.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SKC9
#13: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B


Mass: 12462.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94C12

-
Non-polymers , 3 types, 3 molecules

#14: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#15: Chemical ChemComp-PC7 / (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 1-PALMITOYL-2-STEAROYL-PC / Phosphatidylcholine


Mass: 763.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#16: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N2O8PS

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Arabidopsis complex I - membrane tip / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459177 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313067
ELECTRON MICROSCOPYf_angle_d0.58417667
ELECTRON MICROSCOPYf_dihedral_angle_d7.7421790
ELECTRON MICROSCOPYf_chiral_restr0.0411926
ELECTRON MICROSCOPYf_plane_restr0.0052201

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more