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- PDB-6bw3: Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide -

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Basic information

Entry
Database: PDB / ID: 6bw3
TitleCrystal structure of RBBP4 in complex with PRDM3 N-terminal peptide
Components
  • Histone-binding protein RBBP4
  • MDS1 and EVI1 complex locus protein MDS1
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 / [histone H3]-lysine9 N-methyltransferase / CAF-1 complex / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / Formation of the nephric duct / NURF complex / NuRD complex / regulation of cell fate specification ...histone H3K9 monomethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / CAF-1 complex / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / Formation of the nephric duct / NURF complex / NuRD 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 / negative regulation of programmed cell death / negative regulation of JNK cascade / histone H3 methyltransferase activity / hematopoietic stem cell proliferation / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / Transcriptional Regulation by E2F6 / positive regulation of stem cell population maintenance / histone deacetylase complex / RNA Polymerase I Transcription Initiation / 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 cell migration / Regulation of PTEN gene transcription / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / Oxidative Stress Induced Senescence / histone binding / methylation / Potential therapeutics for SARS / chromosome, telomeric region / DNA replication / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
PRDM3, 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 ...PRDM3, 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 / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Zinc finger C2H2-type / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Mainly Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase MECOM / Histone-binding protein RBBP4 / Histone-lysine N-methyltransferase MECOM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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: MDS1 and EVI1 complex locus protein MDS1
A: Histone-binding protein RBBP4
D: MDS1 and EVI1 complex locus protein MDS1


Theoretical massNumber of molelcules
Total (without water)98,46716
Polymers98,4674
Non-polymers012
Water1,982110
1
C: Histone-binding protein RBBP4
B: MDS1 and EVI1 complex locus protein MDS1


Theoretical massNumber of molelcules
Total (without water)49,2336
Polymers49,2332
Non-polymers04
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint0 kcal/mol
Surface area15750 Å2
MethodPISA
2
A: Histone-binding protein RBBP4
D: MDS1 and EVI1 complex locus protein MDS1


Theoretical massNumber of molelcules
Total (without water)49,23310
Polymers49,2332
Non-polymers08
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-1 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.979, 59.822, 101.773
Angle α, β, γ (deg.)90.00, 94.55, 90.00
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: 10 - 410 / Label seq-ID: 12 - 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 MDS1 and EVI1 complex locus protein MDS1 / Myelodysplasia syndrome 1 protein / Myelodysplasia syndrome-associated protein 1


Mass: 1379.699 Da / Num. of mol.: 2 / Fragment: N-terminal residues 1-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13465, UniProt: Q03112*PLUS
#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.: 110 / 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: 47.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG3350, 0.2 M sodium malonate, 0.1 M BisTris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→46.95 Å / Num. obs: 46303 / % possible obs: 99.4 % / Redundancy: 4.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.056 / Rrim(I) all: 0.114 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.2740.99139520.6810.5591.14198.4
9.07-46.953.70.0217020.9310.0140.02597.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xu7

2xu7


Resolution: 2.2→46.95 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.958 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.203 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24594 2217 4.8 %RANDOM
Rwork0.21521 ---
obs0.21671 44059 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.608 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20.43 Å2
2---0.82 Å20 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 2.2→46.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5841 0 12 110 5963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196011
X-RAY DIFFRACTIONr_bond_other_d0.0020.025182
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9248220
X-RAY DIFFRACTIONr_angle_other_deg0.965312022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9315758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88524.753263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21615896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8411520
X-RAY DIFFRACTIONr_chiral_restr0.090.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021185
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5361.6973050
X-RAY DIFFRACTIONr_mcbond_other0.5361.6973049
X-RAY DIFFRACTIONr_mcangle_it0.942.5373799
X-RAY DIFFRACTIONr_mcangle_other0.942.5383800
X-RAY DIFFRACTIONr_scbond_it0.4171.6532961
X-RAY DIFFRACTIONr_scbond_other0.4171.6532962
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6952.4774420
X-RAY DIFFRACTIONr_long_range_B_refined3.31219.0386197
X-RAY DIFFRACTIONr_long_range_B_other3.30518.9946190
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23148 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1C
2A
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 145 -
Rwork0.312 3198 -
obs--98.29 %
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)
11.49390.19610.28962.66860.51931.98540.0930.077-0.00580.10570.0126-0.1783-0.0272-0.0036-0.10570.37390.0157-0.16030.00730.00910.1441-6.097218.438-15.4722
20.14820.4488-1.13221.6348-4.117610.3953-0.06020.00870.0430.035-0.0284-0.0406-0.1022-0.01990.08860.29610.0002-0.00540.36010.03390.3692-8.762134.2203-21.7193
31.86370.13890.44513.0392-0.38352.1998-0.0792-0.2055-0.08540.58430.12770.0771-0.1256-0.2424-0.04850.50740.0466-0.14610.04440.01140.0774-32.5742-9.0462-34.3418
40.1213-0.4841-0.06112.11381.30238.40050.0019-0.00050.01620.0668-0.0348-0.0559-0.1968-0.93970.03290.39450.0088-0.02920.3634-0.03030.3589-34.60665.821-27.7814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C10 - 410
2X-RAY DIFFRACTION2B1 - 10
3X-RAY DIFFRACTION3A9 - 410
4X-RAY DIFFRACTION4D1 - 10

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