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- PDB-6zwk: Crystal structure of the phosphorylated C-terminal tail of histon... -

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Basic information

Entry
Database: PDB / ID: 6zwk
TitleCrystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody)
Components
  • Histone H2AX
  • gammaXbody
KeywordsIMMUNE SYSTEM / NANOBODY / PHOSPHOPEPTIDE-RECOGNITION PROTEIN / GAMMA-H2AX
Function / homology
Function and homology information


chromatin-protein adaptor activity / XY body / protein localization to site of double-strand break / response to ionizing radiation / site of DNA damage / Replacement of protamines by nucleosomes in the male pronucleus / 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 ...chromatin-protein adaptor activity / XY body / protein localization to site of double-strand break / response to ionizing radiation / site of DNA damage / Replacement of protamines by nucleosomes in the male pronucleus / 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 / nucleosomal DNA binding / 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 / RNA Polymerase I Promoter Opening / positive regulation of DNA repair / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / DNA damage checkpoint signaling / PRC2 methylates histones and DNA / condensed nuclear chromosome / male germ cell nucleus / replication fork / Regulation of endogenous retroelements by KRAB-ZFP proteins / meiotic cell cycle / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / double-strand break repair via homologous recombination / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / cellular response to gamma radiation / heterochromatin formation / cerebral cortex development / 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 / structural constituent of chromatin / cellular senescence / nucleosome / double-strand break repair / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / damaged DNA binding / nuclear speck / protein heterodimerization activity / Amyloid fiber formation / centrosome / DNA damage response / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
Histone H2A conserved site / Histone H2A signature. / 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
Similarity search - Domain/homology
Biological speciesVicugna pacos (alpaca)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsMcEwen, A.G. / Moeglin, E. / Desplancq, D. / Weiss, E. / Poterszman, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyFRISBI ANR-10-INBS-05 France
CitationJournal: Cancers (Basel) / Year: 2021
Title: A Novel Nanobody Precisely Visualizes Phosphorylated Histone H2AX in Living Cancer Cells under Drug-Induced Replication Stress.
Authors: Moeglin, E. / Desplancq, D. / Stoessel, A. / Massute, C. / Ranniger, J. / McEwen, A.G. / Zeder-Lutz, G. / Oulad-Abdelghani, M. / Chiper, M. / Lafaye, P. / Di Ventura, B. / Didier, P. / Poterszman, A. / Weiss, E.
History
DepositionJul 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gammaXbody
B: gammaXbody
C: gammaXbody
D: gammaXbody
E: gammaXbody
F: gammaXbody
G: Histone H2AX
H: Histone H2AX
I: Histone H2AX
J: Histone H2AX
K: Histone H2AX
L: Histone H2AX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,91520
Polymers106,71912
Non-polymers1968
Water17,655980
1
A: gammaXbody
G: Histone H2AX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8093
Polymers17,7862
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-18 kcal/mol
Surface area6890 Å2
MethodPISA
2
B: gammaXbody
H: Histone H2AX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8093
Polymers17,7862
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-19 kcal/mol
Surface area6880 Å2
MethodPISA
3
C: gammaXbody
I: Histone H2AX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8093
Polymers17,7862
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-17 kcal/mol
Surface area6970 Å2
MethodPISA
4
D: gammaXbody
J: Histone H2AX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8454
Polymers17,7862
Non-polymers582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-18 kcal/mol
Surface area6960 Å2
MethodPISA
5
E: gammaXbody
K: Histone H2AX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8093
Polymers17,7862
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-17 kcal/mol
Surface area7100 Å2
MethodPISA
6
F: gammaXbody
L: Histone H2AX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8324
Polymers17,7862
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-18 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.412, 87.412, 105.409
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody
gammaXbody


Mass: 16577.234 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Nanobody / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein/peptide
Histone H2AX / H2a/x / Histone H2A.X


Mass: 1209.199 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Phosphorylated C-terminal tail of Histone H2AX / Source: (synth.) Homo sapiens (human) / References: UniProt: P16104
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 980 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.2M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 8, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→61.49 Å / Num. obs: 130679 / % possible obs: 99.9 % / Redundancy: 10.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.029 / Rrim(I) all: 0.095 / Net I/σ(I): 12.2 / Num. measured all: 1376764 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.5810.62.2686780264250.6350.7322.384199.9
8.49-61.499.80.04277847950.9990.0140.04537.199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.63 Å61.49 Å
Translation5.63 Å61.49 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIXdev_3915refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LZ0

5lz0


Resolution: 1.55→61.49 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1844 6401 4.91 %
Rwork0.1491 124009 -
obs0.1508 130410 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.74 Å2 / Biso mean: 33.5655 Å2 / Biso min: 16.17 Å2
Refinement stepCycle: final / Resolution: 1.55→61.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 8 992 7202
Biso mean--36.99 41.96 -
Num. residues----806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.570.3412430.330240324275100
1.57-1.590.33622400.306941354375100
1.59-1.610.29831680.291842124380100
1.61-1.630.31792110.282941354346100
1.63-1.650.30141990.26242134412100
1.65-1.670.31962500.238140164266100
1.67-1.690.29372020.231741894391100
1.69-1.720.24961960.21141404336100
1.72-1.750.21041720.241714343100
1.75-1.770.22162790.179540634342100
1.77-1.80.22312070.178341414348100
1.8-1.840.20412520.170440494301100
1.84-1.870.19142100.163741894399100
1.87-1.910.20212040.148141554359100
1.91-1.950.19342120.134341394351100
1.95-20.19331890.138540884277100
2-2.050.17671840.12842014385100
2.05-2.10.17341940.131541884382100
2.1-2.170.1712290.131540694298100
2.17-2.240.16712530.123140934346100
2.24-2.320.17742160.138741594375100
2.32-2.410.18182120.132741534365100
2.41-2.520.20282240.137641134337100
2.52-2.650.19822200.142141554375100
2.65-2.820.16892170.134541154332100
2.82-3.030.1841520.149942044356100
3.03-3.340.17042140.140141404354100
3.34-3.820.14482500.128340834333100
3.82-4.810.15171990.121341664365100
4.82-61.490.18482030.16044103430699

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