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- PDB-6kvd: Crystal structure of human nucleosome containing H2A.J -

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Basic information

Entry
Database: PDB / ID: 6kvd
TitleCrystal structure of human nucleosome containing H2A.J
Components
  • DNA (146-MER)
  • Histone H2A.J
  • Histone H2B type 1-J
  • Histone H3.1Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / nucleosome / histone variant / chromatin / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine ...negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / Packaging Of Telomere Ends / 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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / 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 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / antibacterial humoral response / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / defense response to Gram-negative bacterium / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / 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
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2B type 1-J / Histone H4 / Histone H3.1 / Histone H2A.J
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsTanaka, H. / Koyama, M. / Sato, S. / Kujirai, T. / Kurumizaka, H.
Funding support Japan, 8items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP17H01408 Japan
Japan Society for the Promotion of ScienceJP18H05534 Japan
Japan Society for the Promotion of ScienceJP18K14677 Japan
Japan Society for the Promotion of ScienceJP19K21177 Japan
Japan Society for the Promotion of ScienceJP19K06609 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101076 Japan
Japan Science and TechnologyJPMJCR16G1 Japan
Japan Society for the Promotion of ScienceJP18J13668 Japan
CitationJournal: J.Biochem. / Year: 2020
Title: Biochemical and structural analyses of the nucleosome containing human histone H2A.J.
Authors: Tanaka, H. / Sato, S. / Koyama, M. / Kujirai, T. / Kurumizaka, H.
History
DepositionSep 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
I: DNA (146-MER)
J: DNA (146-MER)
A: Histone H3.1
B: Histone H4
C: Histone H2A.J
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A.J
H: Histone H2B type 1-J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,85127
Polymers201,99410
Non-polymers85617
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58700 Å2
ΔGint-498 kcal/mol
Surface area72500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.640, 108.791, 171.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain E
12chain B
22chain F
13chain C
23chain G
14chain D
24chain H
15chain I
25chain J

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLUGLUchain AAC38 - 13342 - 137
21LYSLYSARGARGchain EEG36 - 13440 - 138
12ASNASNGLYGLYchain BBD25 - 10129 - 105
22HISHISGLYGLYchain FFH18 - 10222 - 106
13ARGARGPROPROchain CCE11 - 11715 - 121
23ALAALALYSLYSchain GGI14 - 11818 - 122
14SERSERALAALAchain DDF32 - 12436 - 128
24SERSERSERSERchain HHJ32 - 12336 - 127
15DADADTDTchain IIA1 - 1461 - 146
25DADADTDTchain JJB147 - 2921 - 146

NCS ensembles :
ID
1
2
3
4
5

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Components

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DNA chain , 1 types, 2 molecules IJ

#1: DNA chain DNA (146-MER)


Mass: 45053.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli DH5a (bacteria)

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein Histone H3.1 / Histone H3 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15719.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68431
#3: Protein Histone H4 /


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62805
#4: Protein Histone H2A.J / H2a/j


Mass: 14329.728 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AFJ / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BTM1
#5: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06899

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Non-polymers , 3 types, 309 molecules

#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: potassium cacodylate, potassium chloride, manganese chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 25, 2018
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 93881 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 48.185 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.176 / Rrim(I) all: 0.183 / Χ2: 1.027 / Net I/σ(I): 13.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.21-2.3414.3992.0041.2521472215001149120.522.07799.4
2.34-2.514.4361.2422.1720382514119141190.711.287100
2.5-2.714.1730.7993.6318690813188131880.8790.829100
2.7-2.9614.0020.4796.3416992712136121360.9590.497100
2.96-3.3113.8580.21812.6615306711045110450.9940.227100
3.31-3.8212.6560.12420.89123683977397730.9960.129100
3.82-4.6713.5740.07332.45113083833183310.9980.076100
4.67-6.5714.4210.06438.0994504655365530.9990.066100
6.57-47.83513.1650.04748.9450344383938240.9990.04999.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSJan 26, 2018 BUILT=20180808data reduction
XDSJan 26, 2018 BUILT=20180808data scaling
PDB_EXTRACT3.25data extraction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y0C

5y0c


Resolution: 2.21→47.835 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 4685 5 %
Rwork0.2127 88995 -
obs0.215 93680 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.63 Å2 / Biso mean: 51.0006 Å2 / Biso min: 17.7 Å2
Refinement stepCycle: final / Resolution: 2.21→47.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5979 5983 17 292 12271
Biso mean--62.62 40.16 -
Num. residues----1046
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A596X-RAY DIFFRACTION6.199TORSIONAL
12E596X-RAY DIFFRACTION6.199TORSIONAL
21B476X-RAY DIFFRACTION6.199TORSIONAL
22F476X-RAY DIFFRACTION6.199TORSIONAL
31C638X-RAY DIFFRACTION6.199TORSIONAL
32G638X-RAY DIFFRACTION6.199TORSIONAL
41D558X-RAY DIFFRACTION6.199TORSIONAL
42H558X-RAY DIFFRACTION6.199TORSIONAL
51I2912X-RAY DIFFRACTION6.199TORSIONAL
52J2912X-RAY DIFFRACTION6.199TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.21-2.23510.30741540.2752921
2.2351-2.26140.35021550.32612941
2.2614-2.2890.29151530.27312913
2.289-2.3180.31891550.26542941
2.318-2.34850.2941530.26872919
2.3485-2.38060.29871560.26692954
2.3806-2.41460.34631550.27122946
2.4146-2.45070.30151530.27862917
2.4507-2.4890.33591550.27592943
2.489-2.52980.34011550.26382939
2.5298-2.57340.32711540.2552921
2.5734-2.62020.31221550.25082938
2.6202-2.67060.28211560.24442965
2.6706-2.72510.30361550.24152949
2.7251-2.78430.33191560.24652963
2.7843-2.84910.27491550.25032950
2.8491-2.92030.30571550.24512938
2.9203-2.99930.31341550.25292949
2.9993-3.08750.29751550.24992948
3.0875-3.18720.32731570.23372977
3.1872-3.3010.23811560.22452967
3.301-3.43320.24031560.20812969
3.4332-3.58940.25171570.20072969
3.5894-3.77850.26861560.2062974
3.7785-4.01520.24951570.18862988
4.0152-4.3250.21481590.17753012
4.325-4.75990.22281580.17093003
4.7599-5.44780.22411590.17843030
5.4478-6.86050.2631610.19753057
6.8605-47.8350.16621690.16623194

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