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- PDB-2yba: Crystal structure of Nurf55 in complex with histone H3 -

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Basic information

Entry
Database: PDB / ID: 2yba
TitleCrystal structure of Nurf55 in complex with histone H3
Components
  • HISTONE H3
  • PROBABLE HISTONE-BINDING PROTEIN CAF1
KeywordsTRANSCRIPTION / RBBP4 / RBBP7 / RBAP46 / RBAP48 / POLYCOMB / PRC2 / WD40 DOMAIN / HISTONE METHYLATION H3K27 / H3K4 / CHROMATIN REMODELLING
Function / homology
Function and homology information


G0 and Early G1 / HDACs deacetylate histones / Regulation of TP53 Activity through Acetylation / Oxidative Stress Induced Senescence / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / Neddylation / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex ...G0 and Early G1 / HDACs deacetylate histones / Regulation of TP53 Activity through Acetylation / Oxidative Stress Induced Senescence / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / Neddylation / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / eggshell chorion gene amplification / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Myb complex / segment specification / CAF-1 complex / polytene chromosome / facultative heterochromatin formation / nucleosome organization / NURF complex / NuRD complex / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / nucleosomal DNA binding / histone methyltransferase complex / Sin3-type complex / regulation of mitotic cell cycle / heterochromatin formation / nucleosome assembly / structural constituent of chromatin / histone deacetylase binding / nucleosome / chromatin organization / histone binding / transcription regulator complex / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / 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 homodimerization activity / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 ...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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / 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 H3 / Chromatin assembly factor 1 p55 subunit
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSchmitges, F.W. / Prusty, A.B. / Faty, M. / Stutzer, A. / Lingaraju, G.M. / Aiwazian, J. / Sack, R. / Hess, D. / Li, L. / Zhou, S. ...Schmitges, F.W. / Prusty, A.B. / Faty, M. / Stutzer, A. / Lingaraju, G.M. / Aiwazian, J. / Sack, R. / Hess, D. / Li, L. / Zhou, S. / Bunker, R.D. / Wirth, U. / Bouwmeester, T. / Bauer, A. / Ly-Hartig, N. / Zhao, K. / Chan, H. / Gu, J. / Gut, H. / Fischle, W. / Muller, J. / Thoma, N.H.
CitationJournal: Mol.Cell / Year: 2011
Title: Histone Methylation by Prc2 is Inhibited by Active Chromatin Marks
Authors: Schmitges, F.W. / Prusty, A.B. / Faty, M. / Stutzer, A. / Lingaraju, G.M. / Aiwazian, J. / Sack, R. / Hess, D. / Li, L. / Zhou, S. / Bunker, R.D. / Wirth, U. / Bouwmeester, T. / Bauer, A. / ...Authors: Schmitges, F.W. / Prusty, A.B. / Faty, M. / Stutzer, A. / Lingaraju, G.M. / Aiwazian, J. / Sack, R. / Hess, D. / Li, L. / Zhou, S. / Bunker, R.D. / Wirth, U. / Bouwmeester, T. / Bauer, A. / Ly-Hartig, N. / Zhao, K. / Chan, H. / Gu, J. / Gut, H. / Fischle, W. / Muller, J. / Thoma, N.H.
History
DepositionMar 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE HISTONE-BINDING PROTEIN CAF1
B: PROBABLE HISTONE-BINDING PROTEIN CAF1
C: HISTONE H3
D: HISTONE H3


Theoretical massNumber of molelcules
Total (without water)99,6784
Polymers99,6784
Non-polymers00
Water2,594144
1
A: PROBABLE HISTONE-BINDING PROTEIN CAF1
D: HISTONE H3


Theoretical massNumber of molelcules
Total (without water)49,8392
Polymers49,8392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-1.9 kcal/mol
Surface area18220 Å2
MethodPISA
2
B: PROBABLE HISTONE-BINDING PROTEIN CAF1
C: HISTONE H3


Theoretical massNumber of molelcules
Total (without water)49,8392
Polymers49,8392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-1.4 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.980, 88.160, 204.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / DCAF-1 / NURF-55


Mass: 47761.629 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q24572
#2: Protein/peptide HISTONE H3 /


Mass: 2077.415 Da / Num. of mol.: 2 / Fragment: N-TERMINAL TAIL, RESIDUES 2-19 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P02299
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.52 Å3/Da / Density % sol: 51.6 % / Description: NONE
Crystal growDetails: 100 MM SODIUM CITRATE, PH 5.4; 200 MM AMMONIUM ACETATE; 23% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00067
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00067 Å / Relative weight: 1
ReflectionResolution: 2.55→43.23 Å / Num. obs: 32778 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 50.55 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 15.2
Reflection shellResolution: 2.55→2.56 Å / Redundancy: 2.12 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.4 / % possible all: 68.4

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED STRUCTURE OF NURF55

Resolution: 2.55→40.47 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0
Details: NCS REPRESENTATION - RESTRAINT LSSR (-AUTONCS). IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1651 5.05 %RANDOM
Rwork0.182 ---
obs0.184 32690 96.7 %-
Displacement parametersBiso mean: 52.59 Å2
Baniso -1Baniso -2Baniso -3
1-9.1544 Å20 Å20 Å2
2--17.7208 Å20 Å2
3----26.8752 Å2
Refinement stepCycle: LAST / Resolution: 2.55→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6313 0 0 144 6457
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016478HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.138835HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2926SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes185HARMONIC2
X-RAY DIFFRACTIONt_gen_planes923HARMONIC5
X-RAY DIFFRACTIONt_it6478HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion2.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion858SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7101SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.63 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2716 134 5.78 %
Rwork0.2357 2185 -
all0.2378 2319 -
obs--96.7 %

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