4HEA Oxidoreductase date Oct 03, 2012
title Crystal Structure Of The Entire Respiratory Complex I From T Thermophilus
authors R.Baradaran, J.M.Berrisford, G.S.Minhas, L.A.Sazanov
compound source
Molecule: Nadh-Quinone Oxidoreductase Subunit 1
Chain: 1, B
Synonym: Nadh Dehydrogenase I Chain 1, Ndh-1 Subunit 1
Ec: 1.6.5.3
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 2
Chain: 2, C
Synonym: Nadh Dehydrogenase I Chain 2, Ndh-1 Subunit 2
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 3
Chain: 3, D
Synonym: Nadh Dehydrogenase I Chain 3, Ndh-1 Subunit 3
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 4
Chain: 4, E
Synonym: Nadh Dehydrogenase I Chain 4, Ndh-1 Subunit 4
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 5
Chain: 5, F
Synonym: Nadh Dehydrogenase I Chain 5, Ndh-1 Subunit 5
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 6
Chain: 6, G
Synonym: Nadh Dehydrogenase I Subunit 6, Ndh-1 Subunit 6
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 9
Chain: 9, O
Synonym: Nadh Dehydrogenase I Subunit 9, Ndh-1 Subunit 9
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 15
Chain: 7, I
Synonym: Nadh Dehydrogenase I Chain 15, Ndh-1 Subunit 15
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Putative Uncharacterized Protein Ttha1528
Chain: W, X

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 7
Chain: A, P
Synonym: Nadh Dehydrogenase I Chain 7, Ndh-1 Subunit 7
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 10
Chain: J, R
Synonym: Nadh Dehydrogenase I Chain 10, Ndh-1 Subunit 10
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 11
Chain: K, S
Synonym: Nadh Dehydrogenase I Chain 11, Ndh-1 Subunit 11
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 12
Chain: L, T
Synonym: Nadh Dehydrogenase I Chain 12, Ndh-1 Subunit 12
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 13
Chain: M, U
Synonym: Nadh Dehydrogenase I Chain 13, Ndh-1 Subunit 13
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 14
Chain: N, V
Synonym: Nadh Dehydrogenase I Chain 14, Ndh-1 Subunit 14
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit 8
Chain: H, Q
Synonym: Nadh Dehydrogenase I Subunit 8, Ndh-1 Subunit 8
Ec: 1.6.5.3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Other_details: Cytoplasmic Membrane
symmetry Space Group: P 1 21 1
R_factor 0.202 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
96.280 340.890 263.300 90.00 100.57 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand FES, FMN, SF4 enzyme Oxidoreductase E.C.1.6.5.3 BRENDA
subcellular loc. Membrane localization by OPM: Bacterial Gram-negative inner membrane
Gene
Ontology
ChainFunctionProcessComponent
1, B


2, C


3, D


6, G


7, I


A, P


E, 4


F, 5


J, R


M, U


N, V


O, 9


Q, H


S, K


T, L


Primary referenceCrystal structure of the entire respiratory complex I., Baradaran R, Berrisford JM, Minhas GS, Sazanov LA, Nature. 2013 Feb 28;494(7438):443-8. doi: 10.1038/nature11871. Epub 2013 Feb 17. PMID:23417064
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3044 Kb) [Save to disk]
  • Biological Unit Coordinates (4hea.pdb1.gz) 1512 Kb
  • Biological Unit Coordinates (4hea.pdb2.gz) 1516 Kb
  • LPC: Ligand-Protein Contacts for 4HEA
  • CSU: Contacts of Structural Units for 4HEA
  • Structure Factors (1977 Kb)
  • Retrieve 4HEA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4HEA from S2C, [Save to disk]
  • Re-refined 4hea structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4HEA in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4HEA
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4HEA, from MSDmotif at EBI
  • Fold representative 4hea from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4hea_R] [4hea_U] [4hea_4] [4hea_C] [4hea_3] [4hea_2] [4hea_6] [4hea_F] [4hea_P] [4hea_O] [4hea_W] [4hea_7] [4hea_J] [4hea_M] [4hea_D] [4hea_A] [4hea_E] [4hea] [4hea_9] [4hea_V] [4hea_H] [4hea_X] [4hea_1] [4hea_K] [4hea_S] [4hea_I] [4hea_Q] [4hea_N] [4hea_L] [4hea_T] [4hea_G] [4hea_5] [4hea_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4HEA: [Molybdop_Fe4S4] [NADH-G_4Fe-4S_3] [NADH_4Fe-4S ] by SMART
  • Other resources with information on 4HEA
  • Community annotation for 4HEA at PDBWiki (http://pdbwiki.org)

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