5A0Q Hydrolase date Apr 22, 2015
title Cryo-Em Reveals The Conformation Of A Substrate Analogue In 20s Proteasome Core
authors P.C.A.Dafonseca, E.P.Morris
compound source
Molecule: Proteasome Subunit Alpha Type-6
Chain: A, O
Synonym: 27 Kda Prosomal Protein, P27k, Macropain Iota Chai Multicatalytic Endopeptidase Complex Iota Chain, Proteasome Chain;
Ec: 3.4.25.1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Alpha Type-2
Chain: B, P
Synonym: Macropain Subunit C3, Multicatalytic Endopeptidase Subunit C3, Proteasome Component C3;
Ec: 3.4.25.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Alpha Type-4
Chain: C, Q
Synonym: Macropain Subunit C9, Multicatalytic Endopeptidase Subunit C9, Proteasome Component C9, Proteasome Subunit L;
Ec: 3.4.25.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Alpha Type-7
Chain: D, R
Synonym: Proteasome Subunit Rc6-1, Proteasome Subunit Xapc7
Ec: 3.4.25.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Alpha Type-5
Chain: E, S
Synonym: Macropain Zeta Chain, Multicatalytic Endopeptidase Zeta Chain, Proteasome Zeta Chain;
Ec: 3.4.25.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Alpha Type-1
Chain: F, T
Synonym: 30 Kda Prosomal Protein, Pros-30, Macropain Subuni Multicatalytic Endopeptidase Complex Subunit C2, Proteasome C2, Proteasome Nu Chain;
Ec: 3.4.25.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Alpha Type-3
Chain: G, U
Synonym: Macropain Subunit C8, Multicatalytic Endopeptidase Subunit C8, Proteasome Component C8;
Ec: 3.4.25.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Beta Type-6
Chain: H, V
Synonym: Macropain Delta Chain, Multicatalytic Endopeptidas Delta Chain, Proteasome Delta Chain, Proteasome Subunit Y;
Ec: 3.4.25.1
Other_details: Subunit Partially Bound To The Inhibitor Ada Acetyl-(6-Aminohexanoyl)3-(Leucinyl)3-Vinyl-(Methyl)-Sulfon (Adaahx3l3vs);

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Beta Type-7
Chain: I, W
Synonym: Macropain Chain Z, Multicatalytic Endopeptidase Co Chain Z, Proteasome Subunit Z;
Ec: 3.4.25.1
Other_details: Subunit Partially Bound To The Inhibitor Ada Acetyl-(6-Aminohexanoyl)3-(Leucinyl)3-Vinyl-(Methyl)-Sulfon (Adaahx3l3vs);

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Beta Type-3
Chain: J, X
Synonym: Proteasome Chain 13, Proteasome Component C10-II, Theta Chain;
Ec: 3.4.25.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Beta Type-2
Chain: K, Y
Synonym: Macropain Subunit C7-I, Multicatalytic Endopeptida Subunit C7-I, Proteasome Component C7-I;
Ec: 3.4.25.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Beta Type-5
Chain: L, Z
Synonym: Macropain Epsilon Chain, Multicatalytic Endopeptid Complex Epsilon Chain, Proteasome Chain 6, Proteasome Epsil Proteasome Subunit Mb1, Proteasome Subunit X;
Ec: 3.4.25.1
Other_details: Subunit Bound To The Inhibitor Adamantane-Ac Aminohexanoyl)3-(Leucinyl)3-Vinyl-(Methyl)-Sulfone (Adaahx3

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Beta Type-1
Chain: M, a
Synonym: Macropain Subunit C5, Multicatalytic Endopeptidase Subunit C5, Proteasome Component C5, Proteasome Gamma Chain
Ec: 3.4.25.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes

Molecule: Proteasome Subunit Beta Type-4
Chain: N, b
Synonym: 26 Kda Prosomal Protein, Pros-26, Macropain Beta C Multicatalytic Endopeptidase Complex Beta Chain, Proteasome Chain, Proteasome Chain 3, Hsn3;
Ec: 3.4.25.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocytes
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 3.50 Å
ligand KNM enzyme Hydrolase E.C.3.4.25.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • positive regulation of NF-ka...

  • B


    D, R


    F, T


    G, U


    J, X


    K, Y


    M


    N


    O
  • positive regulation of NF-ka...

  • P


    Q, C


    S, E


    V, Z, L, W, H, I


    Primary referenceCryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core., da Fonseca PC, Morris EP, Nat Commun. 2015 Jul 2;6:7573. doi: 10.1038/ncomms8573. PMID:26133119
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (758 Kb) [Save to disk]
  • Biological Unit Coordinates (5a0q.pdb1.gz) 745 Kb
  • LPC: Ligand-Protein Contacts for 5A0Q
  • CSU: Contacts of Structural Units for 5A0Q
  • Retrieve 5A0Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5A0Q from S2C, [Save to disk]
  • View 5A0Q 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 5A0Q
  • 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
  • Fold representative 5a0q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5a0q_N] [5a0q_C] [5a0q_A] [5a0q_W] [5a0q_a] [5a0q_Y] [5a0q_E] [5a0q_b] [5a0q_M] [5a0q_J] [5a0q_U] [5a0q_F] [5a0q_P] [5a0q_R] [5a0q_Z] [5a0q_X] [5a0q_Q] [5a0q_D] [5a0q_H] [5a0q_S] [5a0q_V] [5a0q_I] [5a0q_K] [5a0q_B] [5a0q_G] [5a0q_T] [5a0q_L] [5a0q_O] [5a0q]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5A0Q: [Proteasome_A_N ] by SMART
  • Other resources with information on 5A0Q
  • Community annotation for 5A0Q at PDBWiki (http://pdbwiki.org)

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