4D10 Signaling Protein date Apr 30, 2014
title Crystal Structure Of The Cop9 Signalosome
authors R.D.Bunker, G.M.Lingaraju, N.H.Thoma
compound source
Molecule: Cop9 Signalosome Complex Subunit 1
Chain: A, I
Fragment: Residues 52-527
Synonym: Sgn1, Signalosome Subunit 1, G Protein Pathway Sup Gps-1, Jab1-Containing Signalosome Subunit 1, Protein Mfh;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus

Molecule: Cop9 Signalosome Complex Subunit 2
Chain: B, J
Synonym: Sgn2, Signalosome Subunit 2, Alien Homolog, Jab1-C Signalosome Subunit 2, Thyroid Receptor-Interacting Protein Interacting Protein 15, Trip-15;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus

Molecule: Cop9 Signalosome Complex Subunit 3
Chain: C, K
Synonym: Sgn3, Signalosome Subunit 3, Jab1-Containing Signa Subunit 3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus

Molecule: Cop9 Signalosome Complex Subunit 4
Chain: D, L
Synonym: Sgn4, Signalosome Subunit 4, Jab1-Containing Signa Subunit 4;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus

Molecule: Cop9 Signalosome Complex Subunit 5
Chain: E, M
Fragment: Residues 1-423
Synonym: Sgn5, Signalosome Subunit 5, Jun Activation Domain Protein 1;
Ec: 3.4.-.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus

Molecule: Cop9 Signalosome Complex Subunit 6
Chain: F, N
Synonym: Sgn6, Signalosome Subunit 6, Jab1-Containing Signa Subunit 6, Mov34 Homolog, Vpr-Interacting Protein, Hvip;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus

Molecule: Cop9 Signalosome Complex Subunit 7a
Chain: G, O
Fragment: Residues 1-218
Synonym: Sgn7a, Signalosome Subunit 7a, Dermal Papilla-Deri Protein 10, Jab1-Containing Signalosome Subunit 7a;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus

Molecule: Cop9 Signalosome Complex Subunit 8
Chain: H, P
Synonym: Sgn8, Signalosome Subunit 8, Cop9 Homolog, Hcop9, Aining Signalosome Subunit 8, Sgn8, Signalosome Subunit 8, Molog, Jab1-Containing Signalosome Subunit 8;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 31
R_factor 0.199 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
151.615 151.615 343.069 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.80 Å
ligand ZN enzyme Hydrolase E.C.3.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, I
  • GTPase inhibitor activity


  • D, L


    E, M
  • translation initiation facto...


  • F, N


    J, B


    K, C


    P, H


    Primary referenceCrystal structure of the human COP9 signalosome., Lingaraju GM, Bunker RD, Cavadini S, Hess D, Hassiepen U, Renatus M, Fischer ES, Thoma NH, Nature. 2014 Jul 16. doi: 10.1038/nature13566. PMID:25043011
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1708 Kb) [Save to disk]
  • Biological Unit Coordinates (4d10.pdb1.gz) 823 Kb
  • Biological Unit Coordinates (4d10.pdb2.gz) 883 Kb
  • LPC: Ligand-Protein Contacts for 4D10
  • CSU: Contacts of Structural Units for 4D10
  • Structure Factors (2720 Kb)
  • Retrieve 4D10 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D10 from S2C, [Save to disk]
  • Re-refined 4d10 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4D10 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 4D10
  • 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 4D10, from MSDmotif at EBI
  • Fold representative 4d10 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d10_P] [4d10_O] [4d10_F] [4d10_B] [4d10_D] [4d10_C] [4d10_G] [4d10] [4d10_M] [4d10_A] [4d10_H] [4d10_E] [4d10_N] [4d10_I] [4d10_J] [4d10_K] [4d10_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4D10: [JAB_MPN] [PAM] [PINT ] by SMART
  • Other resources with information on 4D10
  • Community annotation for 4D10 at PDBWiki (http://pdbwiki.org)

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