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- PDB-3nqj: Crystal structure of (CENP-A/H4)2 heterotetramer -

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Basic information

Entry
Database: PDB / ID: 3nqj
TitleCrystal structure of (CENP-A/H4)2 heterotetramer
Components
  • Histone H3-like centromeric protein A
  • Histone H4
KeywordsDNA BINDING PROTEIN / alpha helix / histone fold / centromere
Function / homology
Function and homology information


CENP-A containing chromatin assembly / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin ...CENP-A containing chromatin assembly / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Resolution of Sister Chromatid Cohesion / telomere organization / Meiotic synapsis / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RHO GTPases Activate Formins / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / nucleosome assembly / Separation of Sister Chromatids / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Histone, subunit A / Histone, subunit A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold ...Histone, subunit A / Histone, subunit A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Histone H3-like centromeric protein A / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
Homo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSekulic, N. / Black, B.E.
CitationJournal: Nature / Year: 2010
Title: The structure of (CENP-A-H4)(2) reveals physical features that mark centromeres.
Authors: Sekulic, N. / Bassett, E.A. / Rogers, D.J. / Black, B.E.
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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

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Assembly

Deposited unit
A: Histone H3-like centromeric protein A
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2996
Polymers18,9192
Non-polymers3804
Water2,450136
1
A: Histone H3-like centromeric protein A
B: Histone H4
hetero molecules

A: Histone H3-like centromeric protein A
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,59812
Polymers37,8394
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area9990 Å2
ΔGint-117 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.869, 62.869, 159.512
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Histone H3-like centromeric protein A / Centromere protein A / CENP-A / Centromere autoantigen A


Mass: 9379.032 Da / Num. of mol.: 1 / Fragment: UNP residues 60-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Production host: Escherichia coli (E. coli) / References: UniProt: P49450
#2: Protein Histone H4


Mass: 9540.251 Da / Num. of mol.: 1 / Fragment: UNP residues 21-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo Sapiens (human) / Gene: HIST1H4A, H4/A, H4FA / Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET AT N-TERMINUS WAS INTRODUCED IN SEQUENCE BECAUSE IT IS NEEDED TO INITIATE TRANSCRIPTION

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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: 2.4 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.17 M ammonium sulfate, 0.085 M sodium cacodylate (pH 6.5), 25.5% PEG-8000, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→54.45 Å / Num. all: 11876 / Num. obs: 11585 / % possible obs: 97.56 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.22 % / Rmerge(I) obs: 0.083 / Rsym value: 0.057 / Net I/σ(I): 23.39
Reflection shellResolution: 2.08→2.21 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1825 / Rsym value: 0.535 / % possible all: 87.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NQU

3nqu


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.336 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24141 550 4.8 %RANDOM
Rwork0.1797 ---
all0.18249 11000 --
obs0.18249 10961 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.104 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0.81 Å20 Å2
2---1.63 Å20 Å2
3---2.44 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 20 136 1318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221204
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9781626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3395145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.23220.74154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48915218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4621517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02872
X-RAY DIFFRACTIONr_mcbond_it0.6361.5721
X-RAY DIFFRACTIONr_mcangle_it1.19621157
X-RAY DIFFRACTIONr_scbond_it2.2373483
X-RAY DIFFRACTIONr_scangle_it3.8254.5468
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 36 -
Rwork0.208 771 -
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)
13.9194-0.7914-4.28895.45040.13474.9519-0.2719-0.2361-0.41270.22320.02530.06070.43340.13020.24650.3686-0.1632-0.03880.26060.09470.462-16.108615.53639.1895
29.18710.8002-6.23881.6449-0.88376.5841-0.11970.5343-0.35180.1962-0.04830.06320.4121-0.31780.16810.14640.00870.03710.1947-0.04510.1831-4.466917.4676-3.0661
314.23052.9612-11.04948.21681.347410.3339-0.65360.1307-1.08420.274-0.1744-0.25040.7513-0.18530.8280.5320.13380.08770.16790.09850.2294-2.527111.6437.4629
45.6611-5.3601-2.32587.07414.09922.7596-0.2095-0.3939-0.1120.38780.16720.07850.2585-0.02750.04240.1612-0.04190.0210.16120.04150.1231-12.402925.813414.6913
52.79991.1202-0.82154.06110.89533.8816-0.0462-0.14710.1265-0.06760.002-0.0867-0.0552-0.14630.04420.118-0.0172-0.00830.135-0.03290.1221-19.177440.824211.9966
617.3932-4.695-11.792310.02942.301211.20980.31430.7447-0.0422-0.4691-0.2931-0.30320.647-0.5274-0.02120.2596-0.03580.01040.1285-0.05790.2264-21.847620.73233.6178
71.7507-1.40912.3165.94342.38786.8332-0.0453-0.2959-0.10720.5238-0.17080.46640.3809-0.7180.21620.1447-0.09830.05290.24470.01990.1736-24.195527.338716.2331
84.08711.3224.67738.682-1.515911.8255-0.0078-0.0938-0.11640.284-0.09620.4125-0.212-0.72870.1040.0983-0.0323-0.0120.2312-0.01530.1485-27.567533.98899.2773
913.0179-4.68020.46742.2762-0.31620.856-0.02090.19090.4262-0.0984-0.0796-0.04610.14240.02050.10050.1322-0.03380.02290.13410.00130.1268-11.242326.8154.3738
1012.7015-2.3414-8.17549.8344-3.82958.3169-0.3743-0.8291-0.1659-0.137-0.2495-0.68720.45050.85510.62370.28280.20950.05040.35820.12010.26446.74315.78345.1418
1110.6922-3.33540.508436.81095.228310.863-0.2169-0.64780.28010.335-0.0884-0.99630.23341.06180.30520.12830.0773-0.01530.28240.0360.04991.864422.298312.6272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 71
2X-RAY DIFFRACTION2A72 - 82
3X-RAY DIFFRACTION3A83 - 91
4X-RAY DIFFRACTION4A92 - 106
5X-RAY DIFFRACTION5A107 - 134
6X-RAY DIFFRACTION6B24 - 32
7X-RAY DIFFRACTION7B33 - 44
8X-RAY DIFFRACTION8B45 - 50
9X-RAY DIFFRACTION9B51 - 69
10X-RAY DIFFRACTION10B70 - 81
11X-RAY DIFFRACTION11B82 - 92

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