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- PDB-2fxk: Crystal structure of the macro-domain of human core histone varia... -

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Basic information

Entry
Database: PDB / ID: 2fxk
TitleCrystal structure of the macro-domain of human core histone variant macroH2A1.1 (form A)
ComponentsH2A histone family, member Y isoform 1
KeywordsGENE REGULATION / CHROMATIN / HISTONE / A1PP / MACRO-DOMAIN / P-LOOP
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 chromatin ...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 chromatin / sex-chromosome dosage compensation / positive regulation of endodermal cell differentiation / establishment of protein localization to chromatin / double-stranded methylated DNA binding / Barr body / rDNA binding / negative regulation of protein serine/threonine kinase activity / regulation of oxidative phosphorylation / poly-ADP-D-ribose modification-dependent protein binding / positive regulation of keratinocyte differentiation / protein serine/threonine kinase inhibitor activity / negative regulation of response to oxidative stress / nuclear chromosome / negative regulation of gene expression, epigenetic / site of DNA damage / regulation of lipid metabolic process / pericentric heterochromatin / condensed chromosome / nucleosomal DNA binding / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / heterochromatin formation / 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 / negative regulation of transcription by RNA polymerase II / enzyme binding / 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: 2.54 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
DepositionFeb 6, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 14, 2006ID: 1ZQ0
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H2A histone family, member Y isoform 1
B: H2A histone family, member Y isoform 1


Theoretical massNumber of molelcules
Total (without water)44,5492
Polymers44,5492
Non-polymers00
Water77543
1
A: H2A histone family, member Y isoform 1


Theoretical massNumber of molelcules
Total (without water)22,2741
Polymers22,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: H2A histone family, member Y isoform 1


Theoretical massNumber of molelcules
Total (without water)22,2741
Polymers22,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.770, 98.270, 42.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein H2A histone family, member Y isoform 1


Mass: 22274.334 Da / Num. of mol.: 2 / Mutation: non-histone macro-domain (Residues: 182-369)
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: GenBank: 20336746, UniProt: O75367*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG8000, 0.1M NACL, 0.1M TRIS/ HCL PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9311
20.9311
ReflectionResolution: 2.54→90.91 Å / Num. all: 12857 / Num. obs: 12857 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.079 / Net I/σ(I): 16.12
Reflection shellResolution: 2.54→2.7 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.48 / Num. unique all: 1965 / Rsym value: 0.299 / % possible all: 96.3

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHASERphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZR5

1zr5


Resolution: 2.54→90.91 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 28.464 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 1.065 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 643 5 %RANDOM
Rwork0.207 ---
all0.21 12335 --
obs0.21 12212 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.289 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2--0.22 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.54→90.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 0 43 2853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222876
X-RAY DIFFRACTIONr_bond_other_d0.0010.022656
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9733884
X-RAY DIFFRACTIONr_angle_other_deg0.81436224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0745374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.13625.849106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.40615512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.789154
X-RAY DIFFRACTIONr_chiral_restr0.0850.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02532
X-RAY DIFFRACTIONr_nbd_refined0.2330.2764
X-RAY DIFFRACTIONr_nbd_other0.180.22608
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21445
X-RAY DIFFRACTIONr_nbtor_other0.0910.21842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.070.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3490.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6231.52367
X-RAY DIFFRACTIONr_mcbond_other0.1011.5776
X-RAY DIFFRACTIONr_mcangle_it0.83522984
X-RAY DIFFRACTIONr_scbond_it1.19531172
X-RAY DIFFRACTIONr_scangle_it1.8654.5900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 42 -
Rwork0.323 811 -
obs-811 96.3 %

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