[English] 日本語
Yorodumi
- PDB-2ygv: Conserved N-terminal domain of the yeast Histone Chaperone Asf1 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ygv
TitleConserved N-terminal domain of the yeast Histone Chaperone Asf1 in complex with the C-terminal fragment of Rad53
Components
  • HISTONE CHAPERONE ASF1
  • SERINE/THREONINE-PROTEIN KINASE RAD53
KeywordsCHAPERONE/TRANSFERASE / CHAPERONE-TRANSFERASE COMPLEX / CHECKPOINT / DNA DAMAGE / CHROMATIN
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / meiotic recombination checkpoint signaling / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / dual-specificity kinase / nucleosome disassembly / silent mating-type cassette heterochromatin formation / DNA replication origin binding ...deoxyribonucleoside triphosphate biosynthetic process / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / meiotic recombination checkpoint signaling / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / dual-specificity kinase / nucleosome disassembly / silent mating-type cassette heterochromatin formation / DNA replication origin binding / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication initiation / subtelomeric heterochromatin formation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / protein modification process / protein localization / nucleosome assembly / chromatin organization / histone binding / regulation of gene expression / protein tyrosine kinase activity / chromosome, telomeric region / protein kinase activity / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / chromatin / regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Rad53 / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain ...Serine/threonine-protein kinase Rad53 / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase RAD53 / Histone chaperone ASF1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsJiao, Y. / Seeger, K. / Murciano, B. / Ledu, M.H. / Charbonnier, J.B. / Legrand, P. / Lautrette, A. / Gaubert, A. / Mousson, F. / Guerois, R. ...Jiao, Y. / Seeger, K. / Murciano, B. / Ledu, M.H. / Charbonnier, J.B. / Legrand, P. / Lautrette, A. / Gaubert, A. / Mousson, F. / Guerois, R. / Mann, C. / Ochsenbein, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Surprising Complexity of the Asf1 Histone Chaperone-Rad53 Kinase Interaction
Authors: Jiao, Y. / Seeger, K. / Lautrette, A. / Gaubert, A. / Mousson, F. / Guerois, R. / Mann, C. / Ochsenbein, F.
History
DepositionApr 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HISTONE CHAPERONE ASF1
B: HISTONE CHAPERONE ASF1
C: HISTONE CHAPERONE ASF1
D: HISTONE CHAPERONE ASF1
E: SERINE/THREONINE-PROTEIN KINASE RAD53
F: SERINE/THREONINE-PROTEIN KINASE RAD53
G: SERINE/THREONINE-PROTEIN KINASE RAD53
H: SERINE/THREONINE-PROTEIN KINASE RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,95613
Polymers81,4808
Non-polymers4765
Water30617
1
A: HISTONE CHAPERONE ASF1
E: SERINE/THREONINE-PROTEIN KINASE RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4663
Polymers20,3702
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-16.7 kcal/mol
Surface area10160 Å2
MethodPISA
2
B: HISTONE CHAPERONE ASF1
F: SERINE/THREONINE-PROTEIN KINASE RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5584
Polymers20,3702
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-21.7 kcal/mol
Surface area9270 Å2
MethodPISA
3
C: HISTONE CHAPERONE ASF1
G: SERINE/THREONINE-PROTEIN KINASE RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4663
Polymers20,3702
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-20.2 kcal/mol
Surface area9350 Å2
MethodPISA
4
D: HISTONE CHAPERONE ASF1
H: SERINE/THREONINE-PROTEIN KINASE RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4663
Polymers20,3702
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-16.2 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.240, 98.180, 86.490
Angle α, β, γ (deg.)90.00, 132.49, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
HISTONE CHAPERONE ASF1 / ASF1 / ANTI-SILENCING FUNCTION PROTEIN 1 / YASF1


Mass: 17874.141 Da / Num. of mol.: 4 / Fragment: CONSERVED N-TERMINAL DOMAIN, RESIDUES 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P32447
#2: Protein/peptide
SERINE/THREONINE-PROTEIN KINASE RAD53 / RAD53 / CHK2 HOMOLOG / SERINE-PROTEIN KINASE 1


Mass: 2495.872 Da / Num. of mol.: 4 / Fragment: C-TERMINAL, RESIDUES 800-821 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P22216, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.88 % / Description: NONE
Crystal growpH: 6 / Details: 5% PEG 8000, 0.1M NACACO PH 6, 0.2M MG ACETATE

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.94→38.9 Å / Num. obs: 16378 / % possible obs: 98.7 % / Observed criterion σ(I): 2.36 / Redundancy: 3.96 % / Biso Wilson estimate: 61.41 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 10.59
Reflection shellResolution: 2.94→3.12 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 2.36 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ROC

1roc


Resolution: 2.94→38.9 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.8082 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 809 4.94 %RANDOM
Rwork0.1875 ---
obs0.1908 16377 --
Displacement parametersBiso mean: 54.12 Å2
Baniso -1Baniso -2Baniso -3
1-25.2695 Å20 Å25.2244 Å2
2---34.9154 Å20 Å2
3---9.6459 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: LAST / Resolution: 2.94→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5357 0 26 17 5400
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015490HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.337461HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1877SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes151HARMONIC2
X-RAY DIFFRACTIONt_gen_planes767HARMONIC5
X-RAY DIFFRACTIONt_it5490HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion22.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion704SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5887SEMIHARMONIC4
LS refinement shellResolution: 2.94→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3298 133 4.69 %
Rwork0.2306 2704 -
all0.2352 2837 -

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more