4R7A Gene Regulation date Aug 27, 2014
title Crystal Structure Of Rbbp4 Bound To Phf6 Peptide
authors Z.Liu, F.Li, B.Zhang, S.Li, J.Wu, Y.Shi
compound source
Molecule: Phd Finger Protein 6
Chain: A
Fragment: Unp Residues 157-171
Synonym: Phd-Like Zinc Finger Protein
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: This Sequence Occurs Naturally In Humans

Molecule: Histone-Binding Protein Rbbp4
Chain: B
Synonym: Chromatin Assembly Factor 1 Subunit C, Caf-1 Subun Chromatin Assembly Factor I P48 Subunit, Caf-I 48 Kda Subun P48, Nucleosome-Remodeling Factor Subunit Rbap48, Retinobla Binding Protein 4, Rbbp-4, Retinoblastoma-Binding Protein P
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rbbp4, Rbap48
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 21 21 21
R_factor 0.176 R_Free 0.207
length a length b length c angle alpha angle beta angle gamma
50.630 87.550 95.840 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand GOL enzyme

Primary referenceStructural Basis of Plant Homeodomain Finger 6 (PHF6) Recognition by the Retinoblastoma Binding Protein 4 (RBBP4) Component of the Nucleosome Remodeling and Deacetylase (NuRD) Complex., Liu Z, Li F, Zhang B, Li S, Wu J, Shi Y, J Biol Chem. 2015 Mar 6;290(10):6630-8. doi: 10.1074/jbc.M114.610196. Epub 2015, Jan 19. PMID:25601084
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (4r7a.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 4R7A
  • CSU: Contacts of Structural Units for 4R7A
  • Structure Factors (688 Kb)
  • Retrieve 4R7A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4R7A from S2C, [Save to disk]
  • Re-refined 4r7a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4R7A 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 4R7A
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4R7A, from MSDmotif at EBI
  • Fold representative 4r7a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4r7a_B] [4r7a] [4r7a_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4R7A: [WD40 ] by SMART
  • Other resources with information on 4R7A
  • Community annotation for 4R7A at PDBWiki (http://pdbwiki.org)

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