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- PDB-2xd7: Crystal structure of the macro domain of human core histone H2A -

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Basic information

Entry
Database: PDB / ID: 2xd7
TitleCrystal structure of the macro domain of human core histone H2A
ComponentsCORE HISTONE MACRO-H2A.2
KeywordsDNA BINDING PROTEIN / CHROMOSOMAL PROTEIN / NUCLEOSOME CORE / CHROMATIN REGULATOR / NUCLEUS / DNA-BINDING PROTEIN / PHOSPHOPROTEIN
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 / nucleosomal DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / chromatin DNA binding ...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 / nucleosomal DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / chromatin DNA binding / heterochromatin formation / 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
Core histone macro-H2A.2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsVollmar, M. / Phillips, C. / Carpenter, E.P. / Muniz, J.R.C. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. ...Vollmar, M. / Phillips, C. / Carpenter, E.P. / Muniz, J.R.C. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Gileadi, O.
CitationJournal: To be Published
Title: Crystal Structure of the Macro Domain of Human Core Histone H2A
Authors: Vollmar, M. / Phillipps, C. / Carpenter, E.P. / Muniz, J.R.C. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Gileadi, O.
History
DepositionApr 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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.2
B: CORE HISTONE MACRO-H2A.2
C: CORE HISTONE MACRO-H2A.2
D: CORE HISTONE MACRO-H2A.2


Theoretical massNumber of molelcules
Total (without water)83,3474
Polymers83,3474
Non-polymers00
Water3,171176
1
A: CORE HISTONE MACRO-H2A.2


Theoretical massNumber of molelcules
Total (without water)20,8371
Polymers20,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CORE HISTONE MACRO-H2A.2


Theoretical massNumber of molelcules
Total (without water)20,8371
Polymers20,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CORE HISTONE MACRO-H2A.2


Theoretical massNumber of molelcules
Total (without water)20,8371
Polymers20,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CORE HISTONE MACRO-H2A.2


Theoretical massNumber of molelcules
Total (without water)20,8371
Polymers20,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.030, 61.640, 242.230
Angle α, β, γ (deg.)90.00, 89.64, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31B
41D
12B
22A
32C
42D

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYLEULEUCC178 - 1972 - 21
211GLYGLYLEULEUAA178 - 1972 - 21
311GLYGLYLEULEUBB178 - 1972 - 21
411GLYGLYLEULEUDD178 - 1972 - 21
121GLYGLYGLUGLUCC208 - 24332 - 67
221GLYGLYGLUGLUAA208 - 24332 - 67
321GLYGLYGLUGLUBB208 - 24332 - 67
421GLYGLYGLUGLUDD208 - 24332 - 67
131VALVALLEULEUCC245 - 25569 - 79
231VALVALLEULEUAA245 - 25569 - 79
331VALVALLEULEUBB245 - 25569 - 79
431VALVALLEULEUDD245 - 25569 - 79
141VALVALHISHISCC257 - 27781 - 101
241VALVALHISHISAA257 - 27781 - 101
341VALVALHISHISBB257 - 27781 - 101
441VALVALHISHISDD257 - 27781 - 101
151PROPROLYSLYSCC279 - 368103 - 192
251PROPROLYSLYSAA279 - 368103 - 192
351PROPROLYSLYSBB279 - 368103 - 192
451PROPROLYSLYSDD279 - 368103 - 192
112SERSERGLNGLNBB198 - 20122 - 25
212SERSERGLNGLNAA198 - 20122 - 25
312SERSERGLNGLNCC198 - 20122 - 25
412SERSERGLNGLNDD198 - 20122 - 25
122ILEILEILEILEBB204 - 20728 - 31
222ILEILEILEILEAA204 - 20728 - 31
322ILEILEILEILECC204 - 20728 - 31
422ILEILEILEILEDD204 - 20728 - 31

NCS ensembles :
ID
1
2

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Components

#1: Protein
CORE HISTONE MACRO-H2A.2 / HISTONE MACROH2A2 / MH2A2


Mass: 20836.684 Da / Num. of mol.: 4 / Fragment: MACRO DOMAIN, RESIDUES 177-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNH-TRXT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9P0M6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAINS A AND B START WITH GLY178 CHAINS C AND D START WITH ASP177

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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: 1.75 Å3/Da / Density % sol: 29.84 % / Description: NONE
Crystal growDetails: 0.05M MGCL2; 0.1M HEPES PH 7.5; 30% MPEG 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.563
11h,-k,-l20.437
ReflectionResolution: 2.1→41.86 Å / Num. obs: 45536 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.3 / % possible all: 77.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID

1yd9

1zr3

1zr5

3iid


Resolution: 2.09→40 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.914 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.25298 2281 5 %RANDOM
Rwork0.21743 ---
obs0.21922 43253 90.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.822 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20.32 Å2
2---10.95 Å20 Å2
3---9.02 Å2
Refinement stepCycle: LAST / Resolution: 2.09→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 0 176 5760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225688
X-RAY DIFFRACTIONr_bond_other_d0.0030.023756
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9737690
X-RAY DIFFRACTIONr_angle_other_deg1.31439326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20826.131199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05415969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.436155
X-RAY DIFFRACTIONr_chiral_restr0.0870.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216344
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021014
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
12A1016tight positional0.050.05
13B1016tight positional0.050.05
11C1016tight positional0.050.05
14D1016tight positional0.040.05
22A48tight positional0.030.05
21B48tight positional0.040.05
23C48tight positional0.040.05
24D48tight positional0.050.05
12A1070medium positional0.050.5
13B1070medium positional0.040.5
11C1070medium positional0.050.5
14D1070medium positional0.040.5
22A45medium positional0.060.5
21B45medium positional0.060.5
23C45medium positional0.040.5
24D45medium positional0.050.5
12A1016tight thermal2.850.5
13B1016tight thermal3.020.5
11C1016tight thermal2.250.5
14D1016tight thermal4.90.5
22A48tight thermal2.20.5
21B48tight thermal1.580.5
23C48tight thermal2.230.5
24D48tight thermal2.040.5
12A1070medium thermal3.22
13B1070medium thermal3.482
11C1070medium thermal2.92
14D1070medium thermal4.842
22A45medium thermal6.212
21B45medium thermal4.332
23C45medium thermal3.952
24D45medium thermal7.322
LS refinement shellResolution: 2.087→2.141 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 94 -
Rwork0.312 1803 -
obs--52.5 %
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)
17.1573-3.82984.68687.238-4.71385.71410.3227-0.4256-0.5056-0.14830.07010.23630.2659-0.2125-0.39280.35980.060.06840.283-0.11340.183610.5111-2.361854.5483
22.49940.5425-0.25115.4495-1.55662.6260.02830.156-0.331-0.3903-0.0279-0.3760.40230.3531-0.00040.35630.14080.04050.2952-0.04070.188122.47-13.930840.2324
36.94683.715-1.08856.4681-2.25322.5039-0.12390.57040.0159-0.35590.14370.0454-0.04390.01-0.01980.30690.0932-0.00530.2349-0.04450.013217.1745-2.139938.1987
44.08911.494-1.46325.6449-1.08612.3970.29070.09220.0632-0.0371-0.175-0.0382-0.2830.4204-0.11580.31140.09790.04610.2826-0.07590.057917.79062.40447.5396
510.2068-7.67874.249412.0148-4.61066.38980.12210.3075-0.1868-0.71410.07660.38370.2836-0.1628-0.19860.25060.01940.05730.2794-0.08520.1673-7.2593-14.17527.5473
66.2677-0.6355-0.04213.42271.26394.74450.1629-0.18660.3693-0.01810.07480.4192-0.1766-0.2816-0.23770.29260.08820.05660.22030.00140.149-16.9108-0.733521.7799
77.85782.25891.16736.8522-0.14324.3267-0.047-0.7466-0.0080.370.0937-0.2468-0.28860.23-0.04670.26820.09440.04070.2713-0.06540.0644-5.6253-6.612923.4042
85.17810.04960.87393.71080.51081.7586-0.0597-0.00280.23990.12060.2711-0.3436-0.42190.4059-0.21140.34270.07290.1010.2746-0.05660.1035-1.6649-6.758513.6847
97.44924.0856-3.25416.2457-3.14615.5262-0.03750.45070.1903-0.09590.09620.0763-0.1586-0.1721-0.05870.2904-0.00950.00020.2202-0.09480.114110.332812.467467.1744
101.3662-0.3579-0.51894.7993-0.3412.7907-0.0005-0.08010.36980.3302-0.0091-0.3198-0.38630.36330.00960.3295-0.1257-0.00270.3237-0.05290.156522.46823.758581.5082
114.5807-2.69060.93384.3773-0.31312.2628-0.0786-0.5415-0.13720.35860.11590.11220.0415-0.0109-0.03730.2814-0.08810.06950.2438-0.04680.046817.119312.010383.5316
120.97250.15471.23014.1395-0.36921.65890.20850.0803-0.14670.0286-0.0344-0.06540.21160.1978-0.17410.2999-0.07150.01340.3666-0.07110.105618.2547.564874.2717
134.1167-0.0355-0.98618.7908-4.46286.37950.01-0.352-0.07020.4743-0.00030.2158-0.1158-0.0396-0.00970.352-0.0757-0.05330.3042-0.110.2624-7.43324.4235114.1812
144.54090.87040.74112.37121.16672.95320.18970.113-0.47460.06170.14820.15390.1665-0.2407-0.33790.3295-0.0168-0.03480.3272-0.05150.2243-16.770810.622799.711
156.7423-1.3418-1.47518.51020.02895.61960.26710.6645-0.1223-0.4749-0.0909-0.47940.07410.214-0.17620.2395-0.0291-0.03480.2837-0.1160.1281-6.67617.494798.3094
165.38910.2779-1.14114.4674-0.3143.7610.06220.0959-0.4853-0.0513-0.0946-0.53750.35850.41170.03240.3364-0.0343-0.1140.3026-0.07510.2243-1.655917.7795108.0807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A185 - 229
2X-RAY DIFFRACTION2A230 - 270
3X-RAY DIFFRACTION3A271 - 313
4X-RAY DIFFRACTION4A314 - 367
5X-RAY DIFFRACTION5B185 - 229
6X-RAY DIFFRACTION6B230 - 270
7X-RAY DIFFRACTION7B271 - 313
8X-RAY DIFFRACTION8B314 - 367
9X-RAY DIFFRACTION9C185 - 229
10X-RAY DIFFRACTION10C230 - 270
11X-RAY DIFFRACTION11C271 - 313
12X-RAY DIFFRACTION12C314 - 367
13X-RAY DIFFRACTION13D185 - 229
14X-RAY DIFFRACTION14D230 - 270
15X-RAY DIFFRACTION15D271 - 313
16X-RAY DIFFRACTION16D314 - 367

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