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- PDB-3nqu: Crystal structure of partially trypsinized (CENP-A/H4)2 heterotetramer -

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Basic information

Entry
Database: PDB / ID: 3nqu
TitleCrystal structure of partially trypsinized (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 / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Resolution of Sister Chromatid Cohesion / 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 / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / 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 / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / Separation of Sister Chromatids / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / 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
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: 2.5 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Histone H3-like centromeric protein A
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8987
Polymers27,4182
Non-polymers4805
Water30617
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)55,79714
Polymers54,8364
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area10280 Å2
ΔGint-202 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.457, 61.457, 185.619
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: 16023.630 Da / Num. of mol.: 1
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: 11394.426 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.85 Å3/Da / Density % sol: 33.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 2 M ammonium sulfate, 0.1 M HEPES (pH 7.9), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91983 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91983 Å / Relative weight: 1
ReflectionResolution: 2.5→53.22 Å / Num. all: 7852 / Num. obs: 7136 / % possible obs: 90.88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.154 / Rsym value: 0.121 / Net I/σ(I): 12.15
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.44 / Rsym value: 0.685 / % possible all: 90.5

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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: TRUNCATED CHAINS A AND B OF PDB ENTRY 1KX5

1kx5


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.894 / SU B: 25.448 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.47 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3018 330 4.6 %RANDOM
Rwork0.2363 ---
obs0.23944 6806 91.16 %-
all-7466 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.317 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å2-1.05 Å20 Å2
2---2.11 Å20 Å2
3---3.16 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1126 0 25 17 1168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221189
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9781614
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35421.34652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18515207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.5491514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02863
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6781.5717
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27721152
X-RAY DIFFRACTIONr_scbond_it2.1633472
X-RAY DIFFRACTIONr_scangle_it3.5874.5459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.495→2.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 20 -
Rwork0.282 479 -
obs--88.79 %
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)
1-0.2546-0.859915.212515.342-10.918914.52160.1067-0.13160.3621-0.01280.3877-0.7258-0.63550.1822-0.49440.2757-0.0055-0.0070.3472-0.00160.425547.354838.644312.3843
28.0658-0.31034.62220.44760.35912.2002-0.2440.47790.5023-0.0376-0.0337-0.0912-0.21950.2670.27770.1883-0.0148-0.010.22940.07670.233335.880137.5922-1.3915
315.1019-17.89429.233433.77223.9563-6.7377-0.67151.56790.14230.90590.10170.1935-0.7441.19310.56990.33520.0466-0.06640.3083-0.07020.250934.239842.011110.0753
41.1991-1.77260.01196.065-0.97990.5026-0.1798-0.26860.04080.39180.06710.0107-0.09370.01070.11270.2660.0094-0.01360.2485-0.00290.069947.232320.682415.9238
512.6478-2.6083-1.49656.96-1.92030.9125-0.10050.57250.2026-0.24290.19990.49890.2392-0.1452-0.09930.1633-0.01640.00780.18360.00710.242845.142413.70729.5314
610.542-6.81966.29353.56410.48668.22770.32260.63711.1313-0.3679-0.4987-0.7559-0.06710.44140.17610.2629-0.0524-0.06830.2840.09820.2751.948232.54524.1526
7-1.53981.2533-1.94253.3328-1.661414.92160.2449-0.1730.11020.4519-0.25020.0946-0.25770.51320.00540.23020.0019-0.03080.3213-0.00110.156153.832827.035716.7554
81.0435.4929-2.59418.27440.56113.70070.0720.0548-0.0111-0.2021-0.123-0.1125-0.218-0.00870.05110.20510.00780.02770.37190.10510.04955.442422.08066.9911
93.91524.5678-1.00414.5762-2.18730.93670.23380.35760.1085-0.2314-0.23930.06340.145-0.04910.00550.26410.0525-0.04830.3228-0.03540.017139.969727.34864.3859
1028.1688-9.39124.851914.0693-3.9636-2.6615-0.0844-0.4076-0.47790.9698-0.01480.3315-0.1837-0.28640.09920.20410.15950.02540.3145-0.03240.202322.894236.5744.5719
115.03-0.7737-1.8924.9877-6.18529.5125-0.1124-0.97730.60150.32430.70340.3894-0.053-0.7781-0.5910.04470.06430.02380.4349-0.13370.305927.745135.625211.0089
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 66
2X-RAY DIFFRACTION2A67 - 84
3X-RAY DIFFRACTION3A85 - 93
4X-RAY DIFFRACTION4A94 - 121
5X-RAY DIFFRACTION5A122 - 134
6X-RAY DIFFRACTION6B25 - 33
7X-RAY DIFFRACTION7B34 - 44
8X-RAY DIFFRACTION8B45 - 52
9X-RAY DIFFRACTION9B53 - 67
10X-RAY DIFFRACTION10B68 - 78
11X-RAY DIFFRACTION11B79 - 91

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