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- PDB-6fy5: Crystal structure of the macro domain of human macroh2a2 -

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Basic information

Entry
Database: PDB / ID: 6fy5
TitleCrystal structure of the macro domain of human macroh2a2
ComponentsCore histone macro-H2A.2
KeywordsDNA BINDING PROTEIN / macro domain / histone variant
Function / homology
Function and homology information


negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / sex-chromosome dosage compensation / establishment of protein localization to chromatin / Barr body / positive regulation of keratinocyte differentiation / negative regulation of gene expression, epigenetic / heterochromatin organization / nucleosomal DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development ...negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / sex-chromosome dosage compensation / establishment of protein localization to chromatin / Barr body / positive regulation of keratinocyte differentiation / negative regulation of gene expression, epigenetic / heterochromatin organization / nucleosomal DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome, telomeric region / transcription cis-regulatory region binding / protein heterodimerization activity / chromatin / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
Core histone macro-H2A / Core histone macro-H2A, macro domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 ...Core histone macro-H2A / Core histone macro-H2A, macro domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Core histone macro-H2A.2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHothorn, M.
CitationJournal: EMBO Rep. / Year: 2018
Title: MacroH2A histone variants limit chromatin plasticity through two distinct mechanisms.
Authors: Kozlowski, M. / Corujo, D. / Hothorn, M. / Guberovic, I. / Mandemaker, I.K. / Blessing, C. / Sporn, J. / Gutierrez-Triana, A. / Smith, R. / Portmann, T. / Treier, M. / Scheffzek, K. / Huet, ...Authors: Kozlowski, M. / Corujo, D. / Hothorn, M. / Guberovic, I. / Mandemaker, I.K. / Blessing, C. / Sporn, J. / Gutierrez-Triana, A. / Smith, R. / Portmann, T. / Treier, M. / Scheffzek, K. / Huet, S. / Timinszky, G. / Buschbeck, M. / Ladurner, A.G.
History
DepositionMar 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity / Item: _citation.journal_volume / _entity.formula_weight
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Core histone macro-H2A.2
B: Core histone macro-H2A.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8977
Polymers42,5932
Non-polymers3045
Water3,513195
1
A: Core histone macro-H2A.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4173
Polymers21,2961
Non-polymers1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Core histone macro-H2A.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4794
Polymers21,2961
Non-polymers1833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.750, 41.370, 84.150
Angle α, β, γ (deg.)90.00, 97.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Core histone macro-H2A.2 / mH2A2


Mass: 21296.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AFY2, MACROH2A2 / Plasmid: pETM11 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9P0M6
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 47.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 12.5% (w/v) PEG 1,000, 0.2 M sodium acetate, 0.1 M Mes pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97565 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97565 Å / Relative weight: 1
ReflectionResolution: 1.65→19.69 Å / Num. obs: 46778 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 29.38 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.06 / Net I/σ(I): 13.15
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.25 / Num. unique obs: 2724 / CC1/2: 0.45 / Rrim(I) all: 1.1 / % possible all: 92.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZR3

1zr3


Resolution: 1.65→19.68 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2315 4.97 %RANDOM
Rwork0.215 ---
obs0.216 46616 97.5 %-
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.8068 Å20 Å25.2929 Å2
2---2.6385 Å20 Å2
3----4.1683 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 1.65→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 20 195 3173
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013055HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124111HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1092SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes519HARMONIC5
X-RAY DIFFRACTIONt_it3055HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion17.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion407SEMIHARMONIC5
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_contact3828SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2479 125 4.59 %
Rwork0.2389 2598 -
all0.2393 2723 -
obs--77.86 %

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