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- PDB-3r45: Structure of a CENP-A-Histone H4 Heterodimer in complex with chap... -

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Basic information

Entry
Database: PDB / ID: 3r45
TitleStructure of a CENP-A-Histone H4 Heterodimer in complex with chaperone HJURP
Components
  • Histone H3-like centromeric protein A
  • Histone H4
  • Holliday junction recognition protein
KeywordsNUCLEAR PROTEIN / histone fold / Centromere / CENP-A / Histone Chaperone / HJURP
Function / homology
Function and homology information


regulation of DNA binding / 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 / regulation of protein-containing complex assembly / negative regulation of megakaryocyte differentiation ...regulation of DNA binding / 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 / regulation of protein-containing complex assembly / 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 / chromosome segregation / 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 / kinetochore / 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 / histone binding / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / nucleolus / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2320 / Holliday junction recognition protein, HJURP, central domain / Holliday junction recognition protein-associated repeat / Centromere protein Scm3/HJURP / Centromere protein Scm3 / Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2320 / Holliday junction recognition protein, HJURP, central domain / Holliday junction recognition protein-associated repeat / Centromere protein Scm3/HJURP / Centromere protein Scm3 / Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / 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 / Special / 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 / Holliday junction recognition protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHu, H. / Liu, Y. / Wang, M. / Fang, J. / Huang, H. / Yang, N. / Li, Y. / Wang, J. / Yao, X. / Shi, Y. ...Hu, H. / Liu, Y. / Wang, M. / Fang, J. / Huang, H. / Yang, N. / Li, Y. / Wang, J. / Yao, X. / Shi, Y. / Li, G. / Xu, R.M.
CitationJournal: Genes Dev. / Year: 2011
Title: Structure of a CENP-A-histone H4 heterodimer in complex with chaperone HJURP
Authors: Hu, H. / Liu, Y. / Wang, M. / Fang, J. / Huang, H. / Yang, N. / Li, Y. / Wang, J. / Yao, X. / Shi, Y. / Li, G. / Xu, R.M.
History
DepositionMar 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Nov 1, 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: Histone H3-like centromeric protein A
B: Histone H4
C: Holliday junction recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,40019
Polymers38,8753
Non-polymers1,52516
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-63 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.941, 83.941, 86.773
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number149
Space group name H-MP312
Components on special symmetry positions
IDModelComponents
11A-144-

SO4

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Components

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Protein , 3 types, 3 molecules ABC

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


Mass: 17843.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Plasmid: pETDuet / 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) / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Holliday junction recognition protein / HJURP / 14-3-3-associated AKT substrate / Fetal liver-expressing gene 1 protein / Up-regulated in ...HJURP / 14-3-3-associated AKT substrate / Fetal liver-expressing gene 1 protein / Up-regulated in lung cancer 9


Mass: 9636.992 Da / Num. of mol.: 1 / Fragment: residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HJURP / Plasmid: pET28a-smt3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NCD3

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Non-polymers , 3 types, 50 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 7, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 10958 / Num. obs: 10744 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 44.12 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1099 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NQJ

3nqj


Resolution: 2.6→43.386 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8488 / SU ML: 0.29 / σ(F): 0 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 514 4.79 %RANDOM
Rwork0.1846 ---
all0.1874 10958 --
obs0.1874 10737 97.86 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.605 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 129.23 Å2 / Biso mean: 53.4206 Å2 / Biso min: 16.47 Å2
Baniso -1Baniso -2Baniso -3
1-4.3041 Å2-0 Å2-0 Å2
2--4.3041 Å20 Å2
3----8.6082 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 83 34 1899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061875
X-RAY DIFFRACTIONf_angle_d0.8382521
X-RAY DIFFRACTIONf_chiral_restr0.058272
X-RAY DIFFRACTIONf_plane_restr0.005312
X-RAY DIFFRACTIONf_dihedral_angle_d15.157712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.86170.26391130.20112561267499
2.8617-3.27570.24431310.18772563269499
3.2757-4.12650.281310.15952550268198
4.1265-43.39250.22311390.19682549268896
Refinement TLS params.Method: refined / Origin x: 22.4909 Å / Origin y: 3.3793 Å / Origin z: 24.0981 Å
111213212223313233
T0.1609 Å20.008 Å20.0034 Å2-0.3045 Å20.0133 Å2--0.2431 Å2
L1.1518 °2-0.0132 °21.3793 °2-1.0748 °2-0.9293 °2--3.7491 °2
S-0.1565 Å °0.0707 Å °0.0089 Å °0.0635 Å °0.0149 Å °-0.0725 Å °-0.1597 Å °0.5117 Å °0.1323 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA59 - 140
2X-RAY DIFFRACTION1allB23 - 96
3X-RAY DIFFRACTION1allC14 - 74
4X-RAY DIFFRACTION1allA141 - 158
5X-RAY DIFFRACTION1allB103 - 114
6X-RAY DIFFRACTION1allC81 - 100

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