[English] 日本語
Yorodumi
- PDB-3iif: Crystal structure of the macro domain of human histone macroH2A1.... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of endodermal cell differentiation / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / Barr body / 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 cell cycle G2/M phase transition / positive regulation of endodermal cell differentiation / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / Barr body / 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 / double-stranded methylated DNA binding / regulation of oxidative phosphorylation / sex chromatin / rDNA binding / positive regulation of keratinocyte differentiation / dosage compensation by inactivation of X chromosome / establishment of protein localization to chromatin / poly-ADP-D-ribose modification-dependent protein binding / negative regulation of response to oxidative stress / negative regulation of gene expression, epigenetic / nuclear chromosome / regulation of lipid metabolic process / protein serine/threonine kinase inhibitor activity / pericentric heterochromatin / condensed chromosome / site of DNA damage / nucleosomal DNA binding / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / heterochromatin formation / chromosome, telomeric region / transcription cis-regulatory region binding / protein heterodimerization activity / DNA repair / nucleolus / protein kinase binding / chromatin / 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 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain ...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 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more