4AP4	Ligase Signalling Protein	date	Mar 30, 2012
title	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
authors	A.Plechanovova, R.T.Hay, M.H.Tatham, E.Jaffray, J.H.Naismith
compound		source
Molecule: E3 Ubiquitin Ligase Rnf4 Chain: A Fragment: Residues 131-195,131-195 Synonym: Ring Finger Protein 4, Small Nuclear Ring Finger P Protein Snurf; Ec: 6.3.2.- Engineered: Yes Other_details: The Ring Domain Is Duplicated But As A Fused That Is The Sequence Of The Ring Domain From Rnf4 (Residues 194) Is Linked By A Single Glycine Residue To Another Ring (Residues 131 To 194).;		Organism_scientific: Rattus Norvegicus Organism_common: Norway Rat Organism_taxid: 10116 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ubiquitin-Conjugating Enzyme E2 D1 Chain: B, E Synonym: Ubch5a, Stimulator Of Fe Transport, Sft, Ubc45 Ho Ubch5, Ubiquitin Carrier Protein D1, Ubiquitin-Conjugating E2(17)Kb 1, Ubiquitin-Conjugating Enzyme E2-17 Kda 1, Ubiqu Protein Ligase D1; Ec: 6.3.2.19 Engineered: Yes Mutation: Yes Other_details: Isopeptide Amide Linkage Of C85k On Ubch5a T Ubiquitin Chain B Linked To Chain C (Ubiquitin) Chain E Lin Chain F (Ubiquitin);		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ubiquitin C Chain: C, F Fragment: Residues 76-152 Engineered: Yes Other_details: Isopeptide Amide Linked To Ubch5a (Chain B A E)		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.208 R_Free 0.242
crystal cell	length a length b length c angle alpha angle beta angle gamma 50.480 65.090 189.650 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.21 Å
ligand	ZN	enzyme	Ligase E.C.6.3.2 BRENDA
Gene Ontology	Chain Function Process Component A E, B
Primary reference	Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis., Plechanovova A, Jaffray EG, Tatham MH, Naismith JH, Hay RT, Nature. 2012 Sep 6;489(7414):115-20. PMID:22842904

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (200 Kb) [Save to disk] Biological Unit Coordinates (4ap4.pdb1.gz) 192 Kb LPC: Ligand-Protein Contacts for 4AP4 CSU: Contacts of Structural Units for 4AP4 Structure Factors (223 Kb) Retrieve 4AP4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 4AP4 from S2C, [Save to disk] Re-refined 4ap4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 4AP4 in 3D

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Visual 3D analysis of 4AP4

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 4AP4, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [4ap4] [4ap4_B] [4ap4_A] [4ap4_E] [4ap4_C] [4ap4_F] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 4AP4: [RING] [UBCc] [UBQ ] by SMART

Other resources with information on 4AP4

Community annotation for 4AP4 at PDBWiki (http://pdbwiki.org)

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