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- PDB-3iif: Crystal structure of the macro domain of human histone macroH2A1.... -

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Basic information

Entry
Database: PDB / ID: 3iif
TitleCrystal structure of the macro domain of human histone macroH2A1.1 in complex with ADP-ribose (form B)
ComponentsCore histone macro-H2A.1, Isoform 1
KeywordsGENE REGULATION / Histone / Chromatin / macro domain / Chromatin regulator / Chromosomal protein / DNA-binding / Isopeptide bond / Methylation / Nucleosome core / Nucleus / Phosphoprotein
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
ADENOSINE-5-DIPHOSPHORIBOSE / Core histone macro-H2A.1 / Isoform 1 of Core histone macro-H2A.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHothorn, M. / Bortfeld, M. / Ladurner, A.G. / Scheffzek, K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation.
Authors: Timinszky, G. / Till, S. / Hassa, P.O. / Hothorn, M. / Kustatscher, G. / Nijmeijer, B. / Colombelli, J. / Altmeyer, M. / Stelzer, E.H. / Scheffzek, K. / Hottiger, M.O. / Ladurner, A.G.
History
DepositionJul 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Core histone macro-H2A.1, Isoform 1
B: Core histone macro-H2A.1, Isoform 1
C: Core histone macro-H2A.1, Isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5016
Polymers66,8233
Non-polymers1,6783
Water3,009167
1
A: Core histone macro-H2A.1, Isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8342
Polymers22,2741
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Core histone macro-H2A.1, Isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8342
Polymers22,2741
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Core histone macro-H2A.1, Isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8342
Polymers22,2741
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.610, 129.610, 128.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Core histone macro-H2A.1, Isoform 1 / Histone macroH2A1 / mH2A1 / H2A.y / H2A/y / Medulloblastoma antigen MU-MB-50.205


Mass: 22274.334 Da / Num. of mol.: 3 / Fragment: Macro domain: UNP residues 162-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AFY, MACROH2A1, macroH2A1.1 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O75367-2, UniProt: O75367*PLUS
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.8 M (NH4)2SO4, 0.2 M Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→64.82 Å / Num. all: 46730 / Num. obs: 46730 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 37 Å2 / Rsym value: 0.074 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 3651 / Rsym value: 0.482 / % possible all: 96.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IID

3iid


Resolution: 2.1→64.82 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.087 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20459 2337 5 %RANDOM
Rwork0.18005 ---
obs0.1813 44389 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.855 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→64.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4101 0 108 167 4376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224364
X-RAY DIFFRACTIONr_bond_other_d0.0010.022878
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9995944
X-RAY DIFFRACTIONr_angle_other_deg1.02137145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0185570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76825.796157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55815749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.638156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02812
X-RAY DIFFRACTIONr_nbd_refined0.2120.2832
X-RAY DIFFRACTIONr_nbd_other0.1850.22723
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22097
X-RAY DIFFRACTIONr_nbtor_other0.090.22150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2174
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.841.53562
X-RAY DIFFRACTIONr_mcbond_other0.1621.51133
X-RAY DIFFRACTIONr_mcangle_it1.06824420
X-RAY DIFFRACTIONr_scbond_it1.95231895
X-RAY DIFFRACTIONr_scangle_it2.8834.51511
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 171 -
Rwork0.258 3235 -
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)
119.7084-1.03814.128617.11489.553831.10410.0899-0.8234-0.04621.0390.4246-0.31030.398-0.4043-0.5144-0.2091-0.00520.0749-0.09590.0557-0.176359.3377-14.825417.2963
23.7537-0.6021-1.76781.54550.05663.9556-0.0041-0.0651-0.01710.1605-0.08260.02830.0610.12120.0867-0.1603-0.03460.0401-0.2025-0.0179-0.201142.2392-9.665625.5924
34.1135-0.1878-0.95953.2170.12774.1306-0.06350.3568-0.16-0.0067-0.1308-0.07330.25980.15740.1943-0.2168-0.02250.0455-0.1324-0.046-0.231445.1903-13.736816.4519
424.4001-10.9513-1.47726.3696-1.42184.1898-0.36550.15030.97970.1362-0.1421-0.7302-0.02720.53540.5076-0.1398-0.0153-0.005-0.07570.1044-0.073669.5923-2.1578-3.6359
53.647-1.41310.95423.4856-1.45134.0322-0.0109-0.0626-0.03830.1082-0.055-0.32980.1330.11380.0659-0.22660.0171-0.0151-0.14630.0325-0.141870.0929-13.6498.7659
64.645-3.34356.196617.59241.138231.5819-0.13190.82330.0736-1.3199-0.27910.0457-1.0127-0.74280.4110.12380.18090.16810.19330.05060.082476.7551-13.6625-11.2738
74.8639-2.84732.03285.7358-0.3572.2471-0.05220.23160.5501-0.02190.0444-0.2672-0.22250.2370.0078-0.1531-0.05060.058-0.10440.0017-0.073824.0846.482417.8572
86.1721-0.71422.03036.32042.21819.2281-0.506-0.32731.4665-0.13970.095-0.3091-1.3169-0.01610.4110.10320.01460.0123-0.0966-0.04540.448417.082722.473119.6518
96.5009-0.03360.76893.21240.20712.0195-0.0130.63680.3592-0.29070.0305-0.0602-0.16450.2109-0.0176-0.111-0.01490.0553-0.08560.0251-0.092219.51896.751711.8524
1012.1576-4.2194-1.09723.45551.435321.34830.1440.4245-2.7237-0.40870.01270.98531.96690.2449-0.15670.092-0.0661-0.1021-0.0303-0.01540.474820.1701-8.938121.0186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A181 - 188
2X-RAY DIFFRACTION2A189 - 292
3X-RAY DIFFRACTION3A293 - 363
4X-RAY DIFFRACTION4B183 - 202
5X-RAY DIFFRACTION5B203 - 352
6X-RAY DIFFRACTION6B353 - 364
7X-RAY DIFFRACTION7C181 - 231
8X-RAY DIFFRACTION8C232 - 255
9X-RAY DIFFRACTION9C256 - 353
10X-RAY DIFFRACTION10C354 - 362

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