4R8P Structural Protein Dna date Sep 02, 2014
title Crystal Structure Of The Ring1bbmi1ubch5c Prc1 Ubiquitylat Bound To The Nucleosome Core Particle
authors R.K.Mcginty, R.C.Henrici, S.Tan
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Gene: Histone H3.2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3d

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Gene: Histone H4
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Histone H2a
Chain: C, G
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Gene: Histone H2b 1.1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Dna (147-Mer)
Chain: I
Fragment: Widom 601 147-Mer (+ Strand)
Engineered: Yes

Organism_scientific: Synthetic Dna
Organism_taxid: 32630
Gene: Widom 601 Nucleosome Positioning Sequence
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb101
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pst55

Molecule: Dna (147-Mer)
Chain: J
Fragment: Widom 601 147-Mer (- Strand)
Engineered: Yes

Organism_scientific: Synthetic Dna
Organism_taxid: 32630
Gene: Widom 601 Nucleosome Positioning Sequence
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb101
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pst55

Molecule: Polycomb Complex Protein Bmi-1
Chain: K, M
Fragment: Residues 2-109
Synonym: Polycomb Group Ring Finger Protein 4, Ring Finger 51;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bmi1, Pcgf4, Rnf51
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pst44

Molecule: E3 Ubiquitin-Protein Ligase Ring2, Ubiquitin-Conj Enzyme E2 D3;
Chain: L, N
Fragment: Residues 2-116 Of Ring1b And Residues 2-148 Of Ub
Synonym: Huntingtin-Interacting Protein 2-Interacting Prote Hip2-Interacting Protein 3, Protein Ding, Ring Finger Prote Ring1b, Ring Finger Protein 2, Ring Finger Protein Bap-1, U Carrier Protein D3, Ubiquitin-Conjugating Enzyme E2(17)Kb 3 Ubiquitin-Conjugating Enzyme E2-17 Kda 3, Ubiquitin-Protein D3;
Ec: 6.3.2.-, 6.3.2.19
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bap1, Ding, Hipi3, Ring1b, Ring1b-Ubch5c Fusion, Rnf2 Ubch5c, Ube2d3;
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pst44
symmetry Space Group: C 2 2 21
R_factor 0.197 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.923 180.049 375.251 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.28 Å
ligand ZN enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


N, L


Primary referenceCrystal structure of the PRC1 ubiquitylation module bound to the nucleosome., McGinty RK, Henrici RC, Tan S, Nature. 2014 Oct 30;514(7524):591-6. doi: 10.1038/nature13890. PMID:25355358
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (753 Kb) [Save to disk]
  • Biological Unit Coordinates (4r8p.pdb1.gz) 744 Kb
  • LPC: Ligand-Protein Contacts for 4R8P
  • CSU: Contacts of Structural Units for 4R8P
  • Structure Factors (1617 Kb)
  • Retrieve 4R8P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4R8P from S2C, [Save to disk]
  • Re-refined 4r8p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4R8P 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 4R8P
  • 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 4R8P, from MSDmotif at EBI
  • Fold representative 4r8p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4r8p_J] [4r8p_A] [4r8p_G] [4r8p_D] [4r8p] [4r8p_B] [4r8p_L] [4r8p_F] [4r8p_C] [4r8p_N] [4r8p_H] [4r8p_I] [4r8p_E] [4r8p_M] [4r8p_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4R8P: [H2A] [H2B] [H3] [H4] [RING] [UBCc ] by SMART
  • Other resources with information on 4R8P
  • Community annotation for 4R8P at PDBWiki (http://pdbwiki.org)

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