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- PDB-5xwr: Crystal Structure of RBBP4-peptide complex -

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Basic information

Entry
Database: PDB / ID: 5xwr
TitleCrystal Structure of RBBP4-peptide complex
Components
  • Histone-binding protein RBBP4
  • MET-SER-ARG-ARG-LYS-GLN-ALA-LYS-PRO-GLN-HIS-ILE
KeywordsTRANSCRIPTION / Histone Binding protein / Sall4
Function / homology
Function and homology information


CAF-1 complex / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / ESC/E(Z) complex ...CAF-1 complex / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Polo-like kinase mediated events / embryonic limb morphogenesis / inner cell mass cell proliferation / ventricular septum development / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / positive regulation of stem cell population maintenance / Transcriptional Regulation by E2F6 / somatic stem cell population maintenance / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / heterochromatin / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / neural tube closure / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / histone binding / Oxidative Stress Induced Senescence / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / Zinc finger, C2H2 type / YVTN repeat-like/Quinoprotein amine dehydrogenase / zinc finger / Zinc finger C2H2 type domain profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / Zinc finger, C2H2 type / YVTN repeat-like/Quinoprotein amine dehydrogenase / zinc finger / Zinc finger C2H2 type domain profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone-binding protein RBBP4 / Sal-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsJobichen, C. / Lui, B.H. / Daniel, G.T. / Sivaraman, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Targeting cancer addiction for SALL4 by shifting its transcriptome with a pharmacologic peptide.
Authors: Liu, B.H. / Jobichen, C. / Chia, C.S.B. / Chan, T.H.M. / Tang, J.P. / Chung, T.X.Y. / Li, J. / Poulsen, A. / Hung, A.W. / Koh-Stenta, X. / Tan, Y.S. / Verma, C.S. / Tan, H.K. / Wu, C.S. / ...Authors: Liu, B.H. / Jobichen, C. / Chia, C.S.B. / Chan, T.H.M. / Tang, J.P. / Chung, T.X.Y. / Li, J. / Poulsen, A. / Hung, A.W. / Koh-Stenta, X. / Tan, Y.S. / Verma, C.S. / Tan, H.K. / Wu, C.S. / Li, F. / Hill, J. / Joy, J. / Yang, H. / Chai, L. / Sivaraman, J. / Tenen, D.G.
History
DepositionJun 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-binding protein RBBP4
B: Histone-binding protein RBBP4
C: MET-SER-ARG-ARG-LYS-GLN-ALA-LYS-PRO-GLN-HIS-ILE
D: MET-SER-ARG-ARG-LYS-GLN-ALA-LYS-PRO-GLN-HIS-ILE


Theoretical massNumber of molelcules
Total (without water)102,9204
Polymers102,9204
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-4 kcal/mol
Surface area30720 Å2
Unit cell
Length a, b, c (Å)73.840, 59.860, 101.529
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-binding protein RBBP4 / Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / ...Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / CAF-I p48 / Nucleosome-remodeling factor subunit RBAP48 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48


Mass: 49975.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48
Production host: Autographa californica nucleopolyhedrovirus
References: UniProt: Q09028
#2: Protein/peptide MET-SER-ARG-ARG-LYS-GLN-ALA-LYS-PRO-GLN-HIS-ILE


Mass: 1484.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UJQ4*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris, pH5.5, 25% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.689→35 Å / Num. obs: 23165 / % possible obs: 93.5 % / Redundancy: 3.8 % / Net I/σ(I): 6.1
Reflection shellResolution: 2.69→2.75 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XU7

2xu7


Resolution: 2.69→34.96 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.19
RfactorNum. reflection% reflection
Rfree0.256 2167 9.36 %
Rwork0.192 --
obs0.198 23162 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.69→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6045 0 0 131 6176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096233
X-RAY DIFFRACTIONf_angle_d1.3468510
X-RAY DIFFRACTIONf_dihedral_angle_d14.5822191
X-RAY DIFFRACTIONf_chiral_restr0.057946
X-RAY DIFFRACTIONf_plane_restr0.0071101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6912-2.75840.34961270.25631343X-RAY DIFFRACTION76
2.7584-2.83290.33641420.25041463X-RAY DIFFRACTION83
2.8329-2.91620.32081400.24241421X-RAY DIFFRACTION83
2.9162-3.01030.32841310.22511494X-RAY DIFFRACTION83
3.0103-3.11770.28421420.20811445X-RAY DIFFRACTION83
3.1177-3.24240.26871370.20171489X-RAY DIFFRACTION84
3.2424-3.38980.24671480.18371503X-RAY DIFFRACTION84
3.3898-3.56820.26751370.17441512X-RAY DIFFRACTION87
3.5682-3.79130.23021420.17771544X-RAY DIFFRACTION87
3.7913-4.08340.22741430.17311529X-RAY DIFFRACTION86
4.0834-4.4930.21871480.16181563X-RAY DIFFRACTION88
4.493-5.14010.18771390.16511568X-RAY DIFFRACTION89
5.1401-6.46470.25021510.18211619X-RAY DIFFRACTION90
6.4647-29.41580.24911640.2041663X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 14.1859 Å / Origin y: 5.8777 Å / Origin z: 25.8832 Å
111213212223313233
T0.0453 Å20.0093 Å20.0432 Å2-0.0857 Å20.0123 Å2--0.0741 Å2
L0.2607 °20.0869 °20.2496 °2-0.402 °20.2231 °2--0.4764 °2
S0.0215 Å °-0.0213 Å °0.028 Å °0.063 Å °-0.0161 Å °0.0108 Å °0.0601 Å °-0.0181 Å °-0.0043 Å °
Refinement TLS groupSelection details: ALL

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