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- PDB-1zr5: Crystal structure of the macro-domain of human core histone varia... -

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Basic information

Entry
Database: PDB / ID: 1zr5
TitleCrystal structure of the macro-domain of human core histone variant macroH2A1.2
ComponentsH2AFY protein
KeywordsGENE REGULATION / chromatin / histone / a1pp / macro-domain / p-loop / splicing
Function / homology
Function and homology information


negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / sex-chromosome dosage compensation ...negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / sex-chromosome dosage compensation / sex chromatin / establishment of protein localization to chromatin / positive regulation of endodermal cell differentiation / double-stranded methylated DNA binding / negative regulation of response to oxidative stress / Barr body / rDNA binding / regulation of oxidative phosphorylation / negative regulation of protein serine/threonine kinase activity / protein serine/threonine kinase inhibitor activity / positive regulation of keratinocyte differentiation / poly-ADP-D-ribose modification-dependent protein binding / negative regulation of gene expression, epigenetic / nuclear chromosome / site of DNA damage / heterochromatin organization / regulation of lipid metabolic process / nucleosomal DNA binding / pericentric heterochromatin / epigenetic regulation of gene expression / condensed chromosome / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome, telomeric region / transcription cis-regulatory region binding / protein heterodimerization activity / DNA repair / chromatin / nucleolus / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / 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
Core histone macro-H2A.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsKustatscher, G. / Hothorn, M. / Pugieux, C. / Scheffzek, K. / Ladurner, A.G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Splicing regulates NAD metabolite binding to histone macroH2A.
Authors: Kustatscher, G. / Hothorn, M. / Pugieux, C. / Scheffzek, K. / Ladurner, A.G.
History
DepositionMay 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
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.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H2AFY protein
B: H2AFY protein


Theoretical massNumber of molelcules
Total (without water)45,4142
Polymers45,4142
Non-polymers00
Water1267
1
A: H2AFY protein


Theoretical massNumber of molelcules
Total (without water)22,7071
Polymers22,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: H2AFY protein


Theoretical massNumber of molelcules
Total (without water)22,7071
Polymers22,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.549, 72.258, 144.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASPASPAA179 - 36723 - 211
2PHEPHEBB181 - 36725 - 211
DetailsThe biological assembly is presumably a monomer

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Components

#1: Protein H2AFY protein


Mass: 22706.867 Da / Num. of mol.: 2 / Fragment: non-histone macro-domain (Residues: 161-372)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETM11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O75367
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.3 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 5000MME 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.9→72.36 Å / Num. all: 9957 / Num. obs: 9713 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rsym value: 0.061 / Net I/σ(I): 19.7
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 4.46 / Num. unique all: 1342 / Rsym value: 0.311 / % possible all: 84.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model of macroH2A1.2 based on PDB-ID 1HJZ

1hjz


Resolution: 2.92→72.36 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.881 / SU B: 43.778 / SU ML: 0.372 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27691 487 5 %RANDOM
Rwork0.21343 ---
all0.2165 9225 --
obs0.2165 9225 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.584 Å2
Baniso -1Baniso -2Baniso -3
1-5.97 Å20 Å20 Å2
2---0.77 Å20 Å2
3----5.2 Å2
Refinement stepCycle: LAST / Resolution: 2.92→72.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 0 7 2855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222896
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9823906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39826.075107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.94515535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.66154
X-RAY DIFFRACTIONr_chiral_restr0.1060.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022092
X-RAY DIFFRACTIONr_nbd_refined0.2420.21219
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22018
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.22
X-RAY DIFFRACTIONr_mcbond_it0.5311.51887
X-RAY DIFFRACTIONr_mcangle_it0.96922989
X-RAY DIFFRACTIONr_scbond_it1.22831091
X-RAY DIFFRACTIONr_scangle_it2.1254.5917
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1401 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.060.05
tight thermal0.10.5
LS refinement shellResolution: 2.923→2.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 34 -
Rwork0.314 624 -
obs--100 %
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)
12.8381.3597-1.53345.3062-1.93137.36590.0907-0.2549-0.05860.9171-0.05380.1361-0.3525-0.0556-0.03690.14670.0405-0.04820.07270.0775-0.0197-0.1586.70527.246
22.47551.2059-0.50784.3107-0.56067.43810.0697-0.33320.31880.27970.1197-0.1099-1.08070.3573-0.18940.14310.01540.11130.1217-0.03190.059513.72235.5610.54
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA179 - 36723 - 211
2X-RAY DIFFRACTION2BB181 - 36725 - 211

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