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- PDB-2xyi: Crystal Structure of Nurf55 in complex with a H4 peptide -

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Basic information

Entry
Database: PDB / ID: 2xyi
TitleCrystal Structure of Nurf55 in complex with a H4 peptide
Components
  • HISTONE H4
  • PROBABLE HISTONE-BINDING PROTEIN CAF1
KeywordsTRANSCRIPTION / REPRESSOR / PHOSPHOPROTEIN / WD-REPEAT
Function / homology
Function and homology information


G0 and Early G1 / Regulation of TP53 Activity through Acetylation / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / Neddylation / HDMs demethylate histones / PKMTs methylate histone lysines / eggshell chorion gene amplification / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins ...G0 and Early G1 / Regulation of TP53 Activity through Acetylation / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / Neddylation / HDMs demethylate histones / PKMTs methylate histone lysines / eggshell chorion gene amplification / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / Myb complex / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / segment specification / CAF-1 complex / polytene chromosome / NuRD complex / NURF complex / facultative heterochromatin formation / DNA replication-dependent chromatin assembly / nucleosome organization / ESC/E(Z) complex / nuclear chromosome / Sin3-type complex / histone methyltransferase complex / regulation of mitotic cell cycle / RNA polymerase II transcription regulator complex / histone deacetylase binding / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromosome / chromatin organization / histone binding / transcription regulator complex / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleus
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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. ...Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / 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
DI(HYDROXYETHYL)ETHER / Histone H4 / Chromatin assembly factor 1 p55 subunit
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsStirnimann, C.U. / Nowak, A.J. / Mueller, C.W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Chromatin-Modifying Complex Component Nurf55/P55 Associates with Histones H3, H4 and Polycomb Repressive Complex 2 Subunit Su(Z)12 Through Partially Overlapping Binding Sites.
Authors: Nowak, A.J. / Alfieri, C. / Stirnimann, C.U. / Rybin, V. / Baudin, F. / Ly-Hartig, N. / Lindner, D. / Muller, C.W.
History
DepositionNov 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Oct 9, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.5Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE HISTONE-BINDING PROTEIN CAF1
B: HISTONE H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7387
Polymers50,9432
Non-polymers7955
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint7.2 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.510, 59.210, 65.890
Angle α, β, γ (deg.)90.00, 99.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROBABLE HISTONE-BINDING PROTEIN CAF1 / CHROMATIN ASSEMBLY FACTOR 1 P55 SUBUNIT / CAF-1 P55 SUBUNIT / NUCLEOSOME-REMODELING FACTOR 55 KDA ...CHROMATIN ASSEMBLY FACTOR 1 P55 SUBUNIT / CAF-1 P55 SUBUNIT / NUCLEOSOME-REMODELING FACTOR 55 KDA SUBUNIT / NURF-55


Mass: 48689.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PFASTBACHT / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q24572
#2: Protein/peptide HISTONE H4


Mass: 2253.764 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-46 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P84040
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6 / Details: 35%(V/V) PEG 400, 100MM MES PH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.0085
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0085 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 46472 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 18.64 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.1
Reflection shellResolution: 1.75→1.85 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.1 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C99

3c99


Resolution: 1.75→24.397 Å / SU ML: 0.05 / σ(F): 1.99 / Phase error: 17.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 1859 4 %
Rwork0.161 --
obs0.1624 46467 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.22 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 26.272 Å2
Baniso -1Baniso -2Baniso -3
1--0.8604 Å20 Å2-0.0787 Å2
2---4.7543 Å20 Å2
3---0.313 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 53 398 3609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053418
X-RAY DIFFRACTIONf_angle_d0.9714647
X-RAY DIFFRACTIONf_dihedral_angle_d15.9981275
X-RAY DIFFRACTIONf_chiral_restr0.068501
X-RAY DIFFRACTIONf_plane_restr0.004602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79730.26371400.21573374X-RAY DIFFRACTION97
1.7973-1.85020.19921420.19143390X-RAY DIFFRACTION97
1.8502-1.90990.23111410.17423392X-RAY DIFFRACTION98
1.9099-1.97810.23441410.17123390X-RAY DIFFRACTION98
1.9781-2.05730.2031430.16593429X-RAY DIFFRACTION98
2.0573-2.15080.17991420.15623402X-RAY DIFFRACTION98
2.1508-2.26420.1981420.15643424X-RAY DIFFRACTION98
2.2642-2.40590.22351420.15983402X-RAY DIFFRACTION98
2.4059-2.59150.16721440.16153444X-RAY DIFFRACTION99
2.5915-2.85190.19391440.15233465X-RAY DIFFRACTION99
2.8519-3.26380.21181450.16253469X-RAY DIFFRACTION99
3.2638-4.10880.17371450.13823487X-RAY DIFFRACTION99
4.1088-24.3990.17241480.1593540X-RAY DIFFRACTION99

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