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- PDB-8tx8: Crystal Structure of RBBP4 bound to ZNF512B peptide -

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Basic information

Entry
Database: PDB / ID: 8tx8
TitleCrystal Structure of RBBP4 bound to ZNF512B peptide
Components
  • Histone-binding protein RBBP4
  • Zinc finger protein 512B
KeywordsTRANSCRIPTION / NuRD / chromatin compaction / zinc finger
Function / homology
Function and homology information


CAF-1 complex / NuRD complex / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / ESC/E(Z) complex / regulation of stem cell differentiation / Polo-like kinase mediated events ...CAF-1 complex / NuRD complex / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / ESC/E(Z) complex / regulation of stem cell differentiation / Polo-like kinase mediated events / Transcription of E2F targets under negative control by DREAM complex / RHOV GTPase cycle / ATPase complex / Sin3-type complex / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of miRNA transcription / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / PKMTs methylate histone lysines / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / HCMV Early Events / nucleosome assembly / Oxidative Stress Induced Senescence / histone binding / Potential therapeutics for SARS / chromosome, telomeric region / DNA replication / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / Zinc finger protein 512, C2HC zinc finger / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...: / : / Zinc finger protein 512, C2HC zinc finger / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / OXAMIC ACID / Histone-binding protein RBBP4 / Zinc finger protein 512B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDeshpande, C.N. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner.
Authors: Wunderlich, T.M. / Deshpande, C. / Paasche, L.W. / Friedrich, T. / Diegmuller, F. / Haddad, E. / Kreienbaum, C. / Naseer, H. / Stebel, S.E. / Daus, N. / Leers, J. / Lan, J. / Trinh, V.T. / ...Authors: Wunderlich, T.M. / Deshpande, C. / Paasche, L.W. / Friedrich, T. / Diegmuller, F. / Haddad, E. / Kreienbaum, C. / Naseer, H. / Stebel, S.E. / Daus, N. / Leers, J. / Lan, J. / Trinh, V.T. / Vazquez, O. / Butter, F. / Bartkuhn, M. / Mackay, J.P. / Hake, S.B.
History
DepositionAug 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: 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

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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: Zinc finger protein 512B
D: Zinc finger protein 512B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,10123
Polymers102,9944
Non-polymers1,10719
Water6,071337
1
A: Histone-binding protein RBBP4
D: Zinc finger protein 512B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,06912
Polymers51,4972
Non-polymers57310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-binding protein RBBP4
C: Zinc finger protein 512B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,03111
Polymers51,4972
Non-polymers5349
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.103, 59.582, 101.450
Angle α, β, γ (deg.)90.00, 93.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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 48 kDa subunit / CAF-I p48 / Nucleosome-remodeling factor subunit RBAP48 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48


Mass: 49880.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#2: Protein/peptide Zinc finger protein 512B


Mass: 1616.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96KM6

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Non-polymers , 5 types, 356 molecules

#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Condition Morpheus G2 0.1 M MES/imidazole, pH 6.5, 40% v/v ethylene glycol; 20 % w/v PEG 8000, 0.1 M mixture of carboxylic acids

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.2→46.88 Å / Num. obs: 46352 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 31 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.097 / Rrim(I) all: 0.184 / Net I/σ(I): 6.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.238 / Num. unique obs: 6699 / CC1/2: 0.493 / Rpim(I) all: 0.754 / Rrim(I) all: 1.452 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALAdata scaling
PHASERphasing
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.88 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 2385 5.15 %
Rwork0.2079 --
obs0.2098 46302 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6225 0 38 337 6600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.543
X-RAY DIFFRACTIONf_dihedral_angle_d5.46821
X-RAY DIFFRACTIONf_chiral_restr0.048942
X-RAY DIFFRACTIONf_plane_restr0.0041120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.35471340.33982547X-RAY DIFFRACTION100
2.24-2.290.3571440.31482564X-RAY DIFFRACTION100
2.29-2.350.35761620.29822515X-RAY DIFFRACTION100
2.35-2.410.39451180.28942597X-RAY DIFFRACTION100
2.41-2.470.30021630.2862542X-RAY DIFFRACTION100
2.47-2.540.30671470.26792550X-RAY DIFFRACTION100
2.54-2.630.29391400.25152588X-RAY DIFFRACTION100
2.63-2.720.29341380.24062577X-RAY DIFFRACTION100
2.72-2.830.24831340.22932591X-RAY DIFFRACTION100
2.83-2.960.27431260.22252566X-RAY DIFFRACTION100
2.96-3.110.29491480.21432576X-RAY DIFFRACTION100
3.11-3.310.24841580.1992579X-RAY DIFFRACTION100
3.31-3.560.23781200.17962595X-RAY DIFFRACTION100
3.56-3.920.19271330.17392608X-RAY DIFFRACTION100
3.92-4.490.18271130.15212633X-RAY DIFFRACTION100
4.49-5.650.19061410.15742620X-RAY DIFFRACTION100
5.65-46.880.19751660.20382669X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.553 Å / Origin y: 5.1032 Å / Origin z: -24.9855 Å
111213212223313233
T0.3486 Å20.0327 Å2-0.0292 Å2-0.2411 Å20.0107 Å2--0.247 Å2
L0.4508 °20.4547 °20.2723 °2-0.7374 °20.2944 °2--0.268 °2
S0.008 Å °-0.0545 Å °0.0246 Å °0.1236 Å °-0.0183 Å °0.002 Å °-0.0079 Å °-0.0256 Å °0.0079 Å °
Refinement TLS groupSelection details: all

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