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- PDB-7cj0: Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and... -

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Basic information

Entry
Database: PDB / ID: 7cj0
TitleCrystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD
Components
  • DNA replication licensing factor MCM2
  • DnaJ homolog subfamily C member 9
  • Histone H3.3
  • Histone H4
KeywordsCHAPERONE / Histone chaperone
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Unwinding of DNA / negative regulation of chromosome condensation / Barr body / : / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / pericentric heterochromatin formation / inner kinetochore ...Switching of origins to a post-replicative state / Unwinding of DNA / negative regulation of chromosome condensation / Barr body / : / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / pericentric heterochromatin formation / inner kinetochore / positive regulation of ATP-dependent activity / MCM complex / muscle cell differentiation / double-strand break repair via break-induced replication / mitotic DNA replication initiation / oocyte maturation / protein folding chaperone complex / regulation of DNA-templated DNA replication initiation / nucleosomal DNA binding / nucleus organization / DNA replication origin binding / cochlea development / spermatid development / DNA replication initiation / Activation of the pre-replicative complex / single fertilization / subtelomeric heterochromatin formation / Activation of ATR in response to replication stress / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / heat shock protein binding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / embryo implantation / 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 / cellular response to interleukin-4 / telomere organization / DNA helicase activity / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Assembly of the pre-replicative complex / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / 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 / multicellular organism growth / male gonad development / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / HCMV Early Events / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / single-stranded DNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein-folding chaperone binding / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence
Similarity search - Function
: / : / DNAJC9 HTH domain / DNA replication licensing factor MCM2-like, winged-helix domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site ...: / : / DNAJC9 HTH domain / DNA replication licensing factor MCM2-like, winged-helix domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 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 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA replication licensing factor MCM2 / Histone H4 / Histone H3.3 / DnaJ homolog subfamily C member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBao, H. / Huang, H.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFC1004500 China
National Natural Science Foundation of China (NSFC)the Thousand Young Talents Program China
National Natural Science Foundation of China (NSFC)31800619 China
CitationJournal: Mol.Cell / Year: 2021
Title: DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network.
Authors: Hammond, C.M. / Bao, H. / Hendriks, I.A. / Carraro, M. / Garcia-Nieto, A. / Liu, Y. / Reveron-Gomez, N. / Spanos, C. / Chen, L. / Rappsilber, J. / Nielsen, M.L. / Patel, D.J. / Huang, H. / Groth, A.
History
DepositionJul 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 30, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Histone H3.3
F: Histone H4
G: DNA replication licensing factor MCM2
D: DnaJ homolog subfamily C member 9
B: Histone H3.3
C: Histone H4
H: DNA replication licensing factor MCM2
A: DnaJ homolog subfamily C member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3049
Polymers75,2118
Non-polymers921
Water1,24369
1
E: Histone H3.3
F: Histone H4
G: DNA replication licensing factor MCM2
D: DnaJ homolog subfamily C member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6985
Polymers37,6064
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint-67 kcal/mol
Surface area16420 Å2
MethodPISA
2
B: Histone H3.3
C: Histone H4
H: DNA replication licensing factor MCM2
A: DnaJ homolog subfamily C member 9


Theoretical massNumber of molelcules
Total (without water)37,6064
Polymers37,6064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-69 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.510, 47.510, 616.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 4 types, 8 molecules EBFCGHDA

#1: Protein Histone H3.3


Mass: 9026.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P84243
#2: Protein Histone H4


Mass: 11263.231 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
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62805
#3: Protein DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2 homolog / Nuclear protein BM28


Mass: 7860.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49736, DNA helicase
#4: Protein DnaJ homolog subfamily C member 9 / HDJC9 / DnaJ protein SB73


Mass: 9455.661 Da / Num. of mol.: 2 / Mutation: C243S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJC9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8WXX5

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Non-polymers , 2 types, 70 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 58.48 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.13
ReflectionResolution: 2.24→41.084 Å / Num. obs: 41413 / % possible obs: 99.9 % / Redundancy: 17.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
2.24-2.316.82.0342958199.1
10.02-41.0813.70.043621199

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BNV

5bnv


Resolution: 2.5→41.08 Å / Cross valid method: THROUGHOUT / σ(F): 32.39 / Phase error: 34.6 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2948 1479 4.94 %
Rwork0.2577 28442 -
obs0.2607 29934 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.75 Å2 / Biso mean: 81.1957 Å2 / Biso min: 29.62 Å2
Refinement stepCycle: final / Resolution: 2.5→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4621 0 6 69 4696
Biso mean--82.07 69.03 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024666
X-RAY DIFFRACTIONf_angle_d0.4456245
X-RAY DIFFRACTIONf_chiral_restr0.035689
X-RAY DIFFRACTIONf_plane_restr0.005832
X-RAY DIFFRACTIONf_dihedral_angle_d20.5572926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5003-2.5810.40311080.39822456256496
2.581-2.67330.37391050.36632562266796
2.6733-2.78030.39121460.35172530267695
2.7803-2.90680.33391230.33872487261095
2.9068-3.060.36311580.32242535269394
3.06-3.25160.35851140.31432543265796
3.2516-3.50250.33841430.28172568271195
3.5025-3.85470.28841410.27252572271395
3.8547-4.41190.28751410.21842624276595
4.4119-5.55630.26581430.21562660280395
5.5563-40.34880.26121570.22392905306295

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