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- PDB-6bw4: Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide -

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Basic information

Entry
Database: PDB / ID: 6bw4
TitleCrystal structure of RBBP4 in complex with PRDM16 N-terminal peptide
Components
  • Histone-binding protein RBBP4
  • PR domain zinc finger protein 16
KeywordsGENE REGULATION / NuRD / Complex / Epigenetics / Structural Genomics / Structural Genomics Consortium / SGC / Histone-binding protein / Chromatin regulator / Nucleus / Repressor / WD repeat
Function / homology
Function and homology information


histone H3K9 monomethyltransferase activity / CAF-1 complex / negative regulation of granulocyte differentiation / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly ...histone H3K9 monomethyltransferase activity / CAF-1 complex / negative regulation of granulocyte differentiation / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / 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 / regulation of cellular respiration / aggresome / histone H3 methyltransferase activity / 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 / heterochromatin organization / Cyclin E associated events during G1/S transition / brown fat cell differentiation / 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 / transcription repressor complex / 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 / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / nucleosome assembly / positive regulation of cold-induced thermogenesis / histone binding / methylation / DNA-binding transcription activator activity, RNA polymerase II-specific / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / DNA replication / sequence-specific DNA binding / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / transcription cis-regulatory region binding / 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 / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
PRDM16, PR/SET domain / PR domain zinc finger protein 2, PR domain / C2H2-type zinc finger / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, C2H2 type ...PRDM16, PR/SET domain / PR domain zinc finger protein 2, PR domain / C2H2-type zinc finger / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain profile. / SET domain / 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. / 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 / Histone-lysine N-methyltransferase PRDM16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsIvanochko, D. / Halabelian, L. / Hutchinson, A. / Seitova, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex.
Authors: Ivanochko, D. / Halabelian, L. / Henderson, E. / Savitsky, P. / Jain, H. / Marcon, E. / Duan, S. / Hutchinson, A. / Seitova, A. / Barsyte-Lovejoy, D. / Filippakopoulos, P. / Greenblatt, J. / ...Authors: Ivanochko, D. / Halabelian, L. / Henderson, E. / Savitsky, P. / Jain, H. / Marcon, E. / Duan, S. / Hutchinson, A. / Seitova, A. / Barsyte-Lovejoy, D. / Filippakopoulos, P. / Greenblatt, J. / Lima-Fernandes, E. / Arrowsmith, C.H.
History
DepositionDec 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Histone-binding protein RBBP4
B: PR domain zinc finger protein 16
A: Histone-binding protein RBBP4
D: PR domain zinc finger protein 16


Theoretical massNumber of molelcules
Total (without water)98,55116
Polymers98,5514
Non-polymers012
Water2,018112
1
C: Histone-binding protein RBBP4
B: PR domain zinc finger protein 16


Theoretical massNumber of molelcules
Total (without water)49,2752
Polymers49,2752
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histone-binding protein RBBP4
D: PR domain zinc finger protein 16


Theoretical massNumber of molelcules
Total (without water)49,27514
Polymers49,2752
Non-polymers012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.034, 59.862, 101.843
Angle α, β, γ (deg.)90.000, 94.550, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 9 - 410 / Label seq-ID: 11 - 412

Dom-IDAuth asym-IDLabel asym-ID
1CA
2AC

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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: 47853.652 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 PR domain zinc finger protein 16 / PR domain-containing protein 16 / Transcription factor MEL1 / MDS1/EVI1-like gene 1


Mass: 1421.801 Da / Num. of mol.: 2 / Fragment: N-terminal residues 1-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HAZ2
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 22% PEG3350, 0.2 M Sodium malonate, 0.1 M BisTris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→19.87 Å / Num. obs: 61417 / % possible obs: 99.2 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.033 / Rrim(I) all: 0.067 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.054.10.7381816544830.90.4110.8472.499.3
8.94-19.873.70.02224976770.9990.0120.0264791.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6bw3

6bw3


Resolution: 2→19.87 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 13.237 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 2961 4.8 %RANDOM
Rwork0.1987 ---
obs0.2004 58442 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.26 Å2 / Biso mean: 52.505 Å2 / Biso min: 29.57 Å2
Baniso -1Baniso -2Baniso -3
1-3.23 Å2-0 Å2-0.31 Å2
2---2.88 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 2→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5877 0 12 112 6001
Biso mean--58 47.94 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196040
X-RAY DIFFRACTIONr_bond_other_d0.0020.025199
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9238260
X-RAY DIFFRACTIONr_angle_other_deg0.953312062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7965760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64524.737266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21515896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7931520
X-RAY DIFFRACTIONr_chiral_restr0.090.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216795
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021197
Refine LS restraints NCS

Ens-ID: 1 / Number: 23256 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1C
2A
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 217 -
Rwork0.298 4211 -
all-4428 -
obs--99.33 %
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)
11.53050.26970.2772.57260.59891.95490.08080.10130.02650.09980.0145-0.2463-0.0595-0.0115-0.09530.33960.0119-0.19140.01980.01370.1483-6.082618.4541-15.5305
22.18950.1014-1.02481.8506-3.64648.7491-0.2177-0.03130.17420.0376-0.001-0.0946-0.106-0.10470.21870.3146-0.0098-0.01310.3080.04370.3427-8.292834.0806-22.3211
31.65290.31890.24162.7253-0.34672.0897-0.0469-0.1947-0.04880.48490.06980.0525-0.1262-0.1856-0.02290.48460.0323-0.17230.03730.0070.0909-32.6399-8.7304-34.381
41.252-0.1432-1.30210.26150.634711.7149-0.12210.1403-0.04910.0609-0.0646-0.1239-0.1325-0.48960.18670.26530.0056-0.01230.2342-0.0320.2817-33.84265.6404-28.5792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C9 - 410
2X-RAY DIFFRACTION2B1 - 10
3X-RAY DIFFRACTION3A4 - 410
4X-RAY DIFFRACTION4D1 - 10

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