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- PDB-5y1u: Crystal structure of RBBP4 bound to AEBP2 RRK motif -

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Basic information

Entry
Database: PDB / ID: 5y1u
TitleCrystal structure of RBBP4 bound to AEBP2 RRK motif
Components
  • Histone-binding protein RBBP4
  • Zinc finger protein AEBP2
KeywordsGENE REGULATION / AEBP2 / RBBP4 / RbAp48 / WD40
Function / homology
Function and homology information


CAF-1 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 / regulation of stem cell differentiation / NuRD complex / ESC/E(Z) complex / Transcription of E2F targets under negative control by DREAM complex ...CAF-1 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 / regulation of stem cell differentiation / NuRD complex / ESC/E(Z) complex / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / Sin3-type complex / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / ATPase complex / 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 / nucleosome binding / 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 / transcription coregulator activity / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / nucleosome assembly / chromatin organization / histone binding / Oxidative Stress Induced Senescence / DNA replication / Potential therapeutics for SARS / 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 / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / 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 ...Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / 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 AEBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.141 Å
AuthorsSun, A. / Li, F. / Wu, J. / Shi, Y.
CitationJournal: Protein Cell / Year: 2017
Title: Structural and biochemical insights into human zinc finger protein AEBP2 reveals interactions with RBBP4
Authors: Sun, A. / Li, F. / Liu, Z. / Jiang, Y. / Zhang, J. / Wu, J. / Shi, Y.
History
DepositionJul 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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 AEBP2
D: Zinc finger protein AEBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2336
Polymers106,0414
Non-polymers1922
Water7,224401
1
A: Histone-binding protein RBBP4
D: Zinc finger protein AEBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1173
Polymers53,0212
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-18 kcal/mol
Surface area16750 Å2
MethodPISA
2
B: Histone-binding protein RBBP4
C: Zinc finger protein AEBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1173
Polymers53,0212
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-17 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.761, 59.452, 102.438
Angle α, β, γ (deg.)90.000, 94.330, 90.000
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: 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 AEBP2 / Adipocyte enhancer-binding protein 2 / AE-binding protein 2


Mass: 1635.042 Da / Num. of mol.: 2 / Fragment: UNP residues 379-390 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6ZN18
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
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: 2.14→40 Å / Num. obs: 50650 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 31.27 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.057 / Rrim(I) all: 0.113 / Χ2: 1.14 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.233.70.6610.7670.3950.7731.072100
2.23-2.323.70.5670.8190.3390.6631.20999.6
2.32-2.423.80.4540.8780.2690.531.086100
2.42-2.553.80.380.90.2240.4431.12299.7
2.55-2.713.80.2580.9480.1510.2991.17100
2.71-2.923.90.1860.9730.1080.2161.20299.8
2.92-3.213.90.1310.9830.0760.1521.18599.9
3.21-3.683.90.0850.9910.0490.0981.091100
3.68-4.633.90.0520.9950.030.061.06799.9
4.63-404.10.0350.9980.0190.041.19199.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFC

3gfc


Resolution: 2.141→36.762 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.17
RfactorNum. reflection% reflection
Rfree0.2186 2447 4.83 %
Rwork0.169 --
obs0.1713 50616 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.78 Å2 / Biso mean: 37.9119 Å2 / Biso min: 16.08 Å2
Refinement stepCycle: final / Resolution: 2.141→36.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6175 0 10 401 6586
Biso mean--73.39 41.12 -
Num. residues----777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076353
X-RAY DIFFRACTIONf_angle_d0.9088656
X-RAY DIFFRACTIONf_chiral_restr0.059948
X-RAY DIFFRACTIONf_plane_restr0.0051118
X-RAY DIFFRACTIONf_dihedral_angle_d14.3273773
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1413-2.1850.29761320.24862480261289
2.185-2.23250.27431440.24628312975100
2.2325-2.28440.30421430.24642868301199
2.2844-2.34150.24171420.227827762918100
2.3415-2.40480.2851400.21828572997100
2.4048-2.47560.27561590.214828523011100
2.4756-2.55550.29461220.204828412963100
2.5555-2.64680.25391460.19528262972100
2.6468-2.75270.26351340.192228612995100
2.7527-2.8780.24111670.185328042971100
2.878-3.02960.24121600.184228503010100
3.0296-3.21930.23471420.173228472989100
3.2193-3.46770.21671520.148128543006100
3.4677-3.81640.19421460.139528713017100
3.8164-4.36790.17521210.130528883009100
4.3679-5.50010.14861280.123929143042100
5.5001-36.7670.19781690.170629493118100
Refinement TLS params.Method: refined / Origin x: 166.083 Å / Origin y: -9.3674 Å / Origin z: 127.353 Å
111213212223313233
T0.2156 Å2-0.0489 Å20.0135 Å2-0.2267 Å2-0.0221 Å2--0.1951 Å2
L0.6782 °2-0.7303 °20.5591 °2-1.1143 °2-0.6255 °2--0.6475 °2
S0.0424 Å °0.0363 Å °-0.0033 Å °-0.168 Å °-0.0245 Å °0.0314 Å °0.0388 Å °0.0483 Å °-0.0257 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA37 - 442
2X-RAY DIFFRACTION1allB35 - 441
3X-RAY DIFFRACTION1allC291 - 295
4X-RAY DIFFRACTION1allD81 - 85
5X-RAY DIFFRACTION1allF1 - 219
6X-RAY DIFFRACTION1allF220 - 403
7X-RAY DIFFRACTION1allE1 - 2

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