5XTB Oxidoreductase Electron Transport date Jun 18, 2017
title Cryo-Em Structure Of Human Respiratory Complex I Matrix Arm
authors J.Gu, M.Wu, M.Yang
compound source
Molecule: Nadh Dehydrogenase [Ubiquinone] Flavoprotein 1, Mitochondrial;
Chain: A
Fragment: Unp Residues 27-457
Synonym: Complex I-51kd,Ci-51kd,Nadh Dehydrogenase Flavopro Nadh-Ubiquinone Oxidoreductase 51 Kda Subunit;
Ec: 1.6.5.3,1.6.99.3
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Mitochondrial;
Chain: B
Synonym: Complex I-23kd,Ci-23kd,Nadh-Ubiquinone Oxidoreduct Subunit,Tyky Subunit;
Ec: 1.6.5.3,1.6.99.3
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Mitochondrial;
Chain: C
Fragment: Unp Residues 58-213
Synonym: Complex I-20kd,Ci-20kd,Nadh-Ubiquinone Oxidoreduct Subunit,Psst Subunit;
Ec: 1.6.5.3,1.6.99.3
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 6;
Chain: E
Fragment: Unp Residues 42-154
Synonym: Complex I-B14,Ci-B14,Lyr Motif-Containing Protein Ubiquinone Oxidoreductase B14 Subunit;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 2;
Chain: F
Fragment: Unp Residues 14-96
Synonym: Complex I-B8,Ci-B8,Nadh-Ubiquinone Oxidoreductase Subunit;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Acyl Carrier Protein, Mitochondrial
Chain: G
Synonym: Acp,Ci-Sdap,Nadh-Ubiquinone Oxidoreductase 9.6 Kda
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 5;
Chain: H
Synonym: Complex I Subunit B13,Complex I-13kd-B,Ci-13kd-B,N Ubiquinone Oxidoreductase 13 Kda-B Subunit;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 7;
Chain: I
Fragment: Unp Residues 4-113
Synonym: Complex I-B14.5a,Ci-B14.5a,Nadh-Ubiquinone Oxidore Subunit B14.5a;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 9, Mitochondrial;
Chain: J
Fragment: Unp Residues 40-375
Synonym: Complex I-39kd,Ci-39kd,Nadh-Ubiquinone Oxidoreduct Subunit;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] Flavoprotein 3, Mitochondrial;
Chain: K
Fragment: Unp Residues 74-106
Synonym: Complex I-9kd,Ci-9kd,Nadh-Ubiquinone Oxidoreductas Subunit,Renal Carcinoma Antigen Ny-Ren-4;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Mitochondrial;
Chain: L
Fragment: Unp Residues 58-175
Synonym: Complex I-18 Kda,Ci-18 Kda,Complex I-Aqdq,Ci-Aqdq, Ubiquinone Oxidoreductase 18 Kda Subunit;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh-Ubiquinone Oxidoreductase 75 Kda Subunit, Mitochondrial;
Chain: M
Fragment: Unp Residues 30-716
Synonym: Complex I-75kd,Ci-75kd
Ec: 1.6.5.3,1.6.99.3
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 12;
Chain: N
Synonym: 13 Kda Differentiation-Associated Protein,Complex Cib17.2,Nadh-Ubiquinone Oxidoreductase Subunit B17.2;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] Flavoprotein 2, Mitochondrial;
Chain: O
Fragment: Unp Residues 36-247
Synonym: Nadh-Ubiquinone Oxidoreductase 24 Kda Subunit
Ec: 1.6.5.3,1.6.99.3
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Mitochondrial;
Chain: P
Fragment: Unp Residues 43-250
Synonym: Complex I-30kd,Ci-30kd,Nadh-Ubiquinone Oxidoreduct Subunit;
Ec: 1.6.5.3,1.6.99.3
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Mitochondrial;
Chain: Q
Fragment: Unp Residues 79-463
Synonym: Complex I-49kd,Ci-49kd,Nadh-Ubiquinone Oxidoreduct Subunit;
Ec: 1.6.5.3,1.6.99.3
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Mitochondrial;
Chain: T
Synonym: Complex I-13kd-A,Ci-13kd-A,Nadh-Ubiquinone Oxidore Kda-A Subunit;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 13;
Chain: W
Fragment: Unp Residues 7-28
Synonym: Cell Death Regulatory Protein Grim-19,Complex I-B1 B16.6,Gene Associated With Retinoic And Interferon-Induced 19 Protein,Gene Associated With Retinoic And Ifn-Induced Mo Protein,Nadh-Ubiquinone Oxidoreductase B16.6 Subunit
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.40 Å
ligand 8Q1, FES, FMN, NDP, SF4 enzyme Oxidoreductase E.C.1.6.5.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A

  • mitochondrial respiratory ch...
    • B


    C


    G


    H


    I


    J


    K


    L


    M


    N


    O


    P


    Q


    T


    Primary referenceArchitecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2., Guo R, Zong S, Wu M, Gu J, Yang M, Cell. 2017 Sep 7;170(6):1247-1257.e12. doi: 10.1016/j.cell.2017.07.050. Epub 2017, Aug 24. PMID:28844695
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (517 Kb) [Save to disk]
  • Biological Unit Coordinates (5xtb.pdb1.gz) 509 Kb
  • LPC: Ligand-Protein Contacts for 5XTB
  • CSU: Contacts of Structural Units for 5XTB
  • Retrieve 5XTB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XTB from S2C, [Save to disk]
    • View 5XTB 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 5XTB
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xtb_C] [5xtb_O] [5xtb_G] [5xtb_W] [5xtb_P] [5xtb_I] [5xtb_B] [5xtb_J] [5xtb_Q] [5xtb_N] [5xtb_F] [5xtb_M] [5xtb_H] [5xtb_A] [5xtb_L] [5xtb_T] [5xtb_E] [5xtb_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5XTB
  • Community annotation for 5XTB at PDBWiki (http://pdbwiki.org)

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