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- PDB-5xxq: Crystal structure of RBBP4: ZNF827 and its function in telomere -

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Basic information

Entry
Database: PDB / ID: 5xxq
TitleCrystal structure of RBBP4: ZNF827 and its function in telomere
Components
  • Histone-binding protein RBBP4
  • Zinc finger protein 827
KeywordsTRANSCRIPTION / ZNF827 / RBBP4 / RbAp48 / WD40
Function / homology
Function and homology information


CAF-1 complex / 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 ...CAF-1 complex / 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 / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / 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 / 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 / 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 / regulation of gene expression / Oxidative Stress Induced Senescence / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / chromatin remodeling / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
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 / Zinc finger protein 827
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSun, A. / Shi, Y.
CitationJournal: To Be Published
Title: Crystal structure of RBBP4: ZNF827 and its function in telomere
Authors: Sun, A. / Shi, Y.
History
DepositionJul 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Nov 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: Zinc finger protein 827
D: Zinc finger protein 827


Theoretical massNumber of molelcules
Total (without water)106,2834
Polymers106,2834
Non-polymers00
Water7,710428
1
A: Histone-binding protein RBBP4
D: Zinc finger protein 827


Theoretical massNumber of molelcules
Total (without water)53,1422
Polymers53,1422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-binding protein RBBP4
C: Zinc finger protein 827


Theoretical massNumber of molelcules
Total (without water)53,1422
Polymers53,1422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.960, 59.780, 102.560
Angle α, β, γ (deg.)90.000, 95.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 51385.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Plasmid: pFastBacTM HT-B / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q09028
#2: Protein/peptide Zinc finger protein 827 /


Mass: 1756.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q17R98*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 43.64 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M MES monohydrate pH 6.5 , 30%(w/v) Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→102.158 Å / Num. all: 62445 / Num. obs: 62445 / % possible obs: 86.2 % / Redundancy: 6 % / Biso Wilson estimate: 17.56 Å2 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Rsym value: 0.105 / Net I/av σ(I): 5.1 / Net I/σ(I): 9.7 / Num. measured all: 376009
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-26.10.4581.25192284900.1970.50.4583.380.8
2-2.1260.31424889280870.1350.3430.3144.481.3
2.12-2.2760.2552.34518775290.1110.280.2555.480.6
2.27-2.455.90.1933.84187270940.0830.210.1936.381.2
2.45-2.695.70.1614.23835866830.070.1760.1617.883.1
2.69-35.60.1215.43609064050.0530.1330.12110.288.1
3-3.475.50.0956.43369861290.0430.1050.09514.495.1
3.47-4.2560.0817.13241653980.0350.0880.08119.498.5
4.25-6.017.30.05410.53089142500.0220.0590.05422.9100
6.01-40.770.04613.31668323800.0190.050.04621.598.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFC

3gfc


Resolution: 1.9→40.7 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 3088 4.96 %
Rwork0.1725 59223 -
obs0.1745 62311 85.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.54 Å2 / Biso mean: 35.2199 Å2 / Biso min: 8.9 Å2
Refinement stepCycle: final / Resolution: 1.9→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6164 0 0 428 6592
Biso mean---35.88 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136343
X-RAY DIFFRACTIONf_angle_d1.2338654
X-RAY DIFFRACTIONf_chiral_restr0.079954
X-RAY DIFFRACTIONf_plane_restr0.0081122
X-RAY DIFFRACTIONf_dihedral_angle_d18.3043770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92970.36191310.31132488261980
1.9297-1.96130.31891330.24892471260480
1.9613-1.99510.30251230.2252540266381
1.9951-2.03140.24161320.19882493262581
2.0314-2.07050.28371400.22212490263080
2.0705-2.11280.22271230.20272520264380
2.1128-2.15870.24511260.18772551267782
2.1587-2.20890.22131170.18892526264381
2.2089-2.26410.28811330.21292473260680
2.2641-2.32540.21731350.18352537267281
2.3254-2.39380.21631190.18052561268081
2.3938-2.4710.23881310.18222541267281
2.471-2.55930.23611340.1862553268782
2.5593-2.66180.2451500.1862562271283
2.6618-2.78290.23451370.18322692282986
2.7829-2.92960.22271610.18182756291788
2.9296-3.11310.25241360.17662893302992
3.1131-3.35330.17391320.16133023315595
3.3533-3.69060.17181750.14343038321397
3.6906-4.22410.18281760.13693110328699
4.2241-5.32010.14011720.127131693341100
5.3201-40.70940.21811720.18063236340899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.05170.22420.31732.06850.25921.90630.01-0.14240.02830.3453-0.04130.16870.0023-0.2148-0.02320.14250.01130.04690.137-0.00710.12258.4753-17.0704220.6976
21.07410.83610.26982.58150.54741.34690.05550.0303-0.03080.45140.0379-0.41690.03560.0836-0.04560.2680.0504-0.13190.1462-0.01040.252785.681110.1356239.5856
38.26770.5041-6.22938.63541.79328.78510.0186-0.07520.01280.3334-0.241-0.49-0.72490.09560.21450.3582-0.0045-0.12920.23360.03080.442184.084226.0257231.6394
46.8934-1.9192-5.95012.19020.97485.41250.42060.20730.69030.0775-0.12350.1926-1.358-0.7074-0.36090.3540.0686-0.08130.3559-0.04270.482156.3728-1.5362230.2297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 410)A6 - 410
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 411)B7 - 411
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 12)C3 - 12
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 12)D3 - 12

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