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Basic information

Entry
Database: PDB / ID: 5c3i
TitleCrystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2
Components
  • DNA replication licensing factor MCM2,MCM2
  • Histone H3.1Histone H3
  • Histone H4
  • Histone chaperone ASF1A
KeywordsREPLICATION / histone / chaperone / ASF1 / MCM protein
Function / homology
Function and homology information


muscle cell differentiation / Switching of origins to a post-replicative state / Unwinding of DNA / histone chaperone activity / nuclear origin of replication recognition complex / DNA replication-dependent chromatin assembly / CMG complex / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation ...muscle cell differentiation / Switching of origins to a post-replicative state / Unwinding of DNA / histone chaperone activity / nuclear origin of replication recognition complex / DNA replication-dependent chromatin assembly / CMG complex / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / DNA repair-dependent chromatin remodeling / regulation of DNA-templated DNA replication initiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / cochlea development / DNA unwinding involved in DNA replication / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / Activation of ATR in response to replication stress / 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 / cellular response to interleukin-4 / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / helicase activity / Defective pyroptosis / Assembly of the pre-replicative complex / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / 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 / osteoblast differentiation / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / single-stranded DNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / DNA helicase / Estrogen-dependent gene expression / DNA replication / chromosome, telomeric region / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / DNA repair / apoptotic process / chromatin binding / chromatin / enzyme binding / ATP hydrolysis activity / protein-containing complex
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / 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 ...Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / 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 / Histone, subunit A / Histone, subunit A / 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 / Nucleic acid-binding, OB-fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA replication licensing factor MCM2 / Histone H4 / Histone H3.1 / Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsWang, H. / Wang, M. / Yang, N. / Xu, R.M.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31210103914 China
National Natural Science Foundation of China34130018 China
MOST2015CB856202 China
CitationJournal: Protein Cell / Year: 2015
Title: Structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2
Authors: Wang, H. / Wang, M. / Yang, N. / Xu, R.M.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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
A: Histone chaperone ASF1A
B: Histone H3.1
C: Histone H4
D: DNA replication licensing factor MCM2,MCM2
E: Histone chaperone ASF1A
F: Histone H3.1
G: Histone H4
H: DNA replication licensing factor MCM2,MCM2
I: Histone chaperone ASF1A
J: Histone H3.1
K: Histone H4
L: DNA replication licensing factor MCM2,MCM2
M: Histone chaperone ASF1A
N: Histone H3.1
O: Histone H4
P: DNA replication licensing factor MCM2,MCM2
Q: Histone chaperone ASF1A
R: Histone H3.1
S: Histone H4
T: DNA replication licensing factor MCM2,MCM2
U: Histone chaperone ASF1A
V: Histone H3.1
W: Histone H4
X: DNA replication licensing factor MCM2,MCM2


Theoretical massNumber of molelcules
Total (without water)347,73024
Polymers347,73024
Non-polymers00
Water0
1
I: Histone chaperone ASF1A
J: Histone H3.1
K: Histone H4
L: DNA replication licensing factor MCM2,MCM2


Theoretical massNumber of molelcules
Total (without water)57,9554
Polymers57,9554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histone chaperone ASF1A
B: Histone H3.1
C: Histone H4
D: DNA replication licensing factor MCM2,MCM2


Theoretical massNumber of molelcules
Total (without water)57,9554
Polymers57,9554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11540 Å2
ΔGint-56 kcal/mol
Surface area19150 Å2
MethodPISA
3
E: Histone chaperone ASF1A
F: Histone H3.1
G: Histone H4
H: DNA replication licensing factor MCM2,MCM2


Theoretical massNumber of molelcules
Total (without water)57,9554
Polymers57,9554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-55 kcal/mol
Surface area19240 Å2
MethodPISA
4
M: Histone chaperone ASF1A
N: Histone H3.1
O: Histone H4
P: DNA replication licensing factor MCM2,MCM2


Theoretical massNumber of molelcules
Total (without water)57,9554
Polymers57,9554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-63 kcal/mol
Surface area17180 Å2
MethodPISA
5
Q: Histone chaperone ASF1A
R: Histone H3.1
S: Histone H4
T: DNA replication licensing factor MCM2,MCM2


Theoretical massNumber of molelcules
Total (without water)57,9554
Polymers57,9554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-61 kcal/mol
Surface area17010 Å2
MethodPISA
6
U: Histone chaperone ASF1A
V: Histone H3.1
W: Histone H4
X: DNA replication licensing factor MCM2,MCM2


Theoretical massNumber of molelcules
Total (without water)57,9554
Polymers57,9554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-58 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.704, 147.704, 261.796
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Histone chaperone ASF1A / Anti-silencing function protein 1 homolog A / hAsf1a / CCG1-interacting factor A / hCIA


Mass: 21375.646 Da / Num. of mol.: 6 / Fragment: UNP residues 1-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, CGI-98, HSPC146 / Plasmid: pRSFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y294
#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: 15437.167 Da / Num. of mol.: 6
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: pCDFDuet / Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#3: Protein
Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 6
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: pCDFDuet / Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#4: Protein
DNA replication licensing factor MCM2,MCM2 / Minichromosome maintenance protein 2 homolog / Nuclear protein BM28


Mass: 9747.712 Da / Num. of mol.: 6 / Fragment: UNP residues 63-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2, BM28, CCNL1, CDCL1, KIAA0030 / Plasmid: pET-28a-smt3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49736, DNA helicase
Sequence detailsSEQUENCE FOR THE UNK RESIDUES OF ENTITY 4 (MCM2) SHOULD BE GRGLGRMRRGLLYDSDEEDEERPARKRRQV. ONLY FEW ...SEQUENCE FOR THE UNK RESIDUES OF ENTITY 4 (MCM2) SHOULD BE GRGLGRMRRGLLYDSDEEDEERPARKRRQV. ONLY FEW DENSITY OF THE REGION IS OBSERVED, WHICH HAS BEEN ASSINGNED UNK D134-140, AND IS SUPPOSED TO BE C-TERMINUS FROM CHAIN D.

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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: 3.17 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.787
11-h,-k,l20.213
ReflectionResolution: 3.5→50 Å / Num. obs: 42834 / % possible obs: 99.8 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.056 / Rrim(I) all: 0.171 / Χ2: 0.972 / Net I/av σ(I): 12.833 / Net I/σ(I): 5.7 / Num. measured all: 389047
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.639.20.6942210.7920.2430.7330.89100
3.63-3.779.20.55242110.8130.1940.5860.946100
3.77-3.949.20.42342310.8960.1480.4490.979100
3.94-4.159.20.32642520.9470.1140.3460.989100
4.15-4.419.20.2442430.9630.0840.2551.101100
4.41-4.759.20.17242740.9850.0590.1821.09599.9
4.75-5.239.20.14642590.9880.050.1551.02499.8
5.23-5.989.10.14643120.9870.0510.1550.96799.7
5.98-7.538.90.11643360.9920.040.1230.97899.6
7.53-508.30.05944950.9970.0210.0630.73898.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata collection
HKL-2000data scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IO5

2io5


Resolution: 3.5→48.99 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.811 / SU B: 24.455 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1987 5 %RANDOM
Rwork0.2156 ---
obs0.2175 37994 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.72 Å2 / Biso mean: 47.324 Å2 / Biso min: 23.74 Å2
Baniso -1Baniso -2Baniso -3
1--7.15 Å20 Å20 Å2
2---7.15 Å20 Å2
3---14.3 Å2
Refinement stepCycle: final / Resolution: 3.5→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17655 0 0 0 17655
Num. residues----2198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01917949
X-RAY DIFFRACTIONr_angle_refined_deg0.9151.96824267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.85152173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.31323.468940
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22153152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5515201
X-RAY DIFFRACTIONr_chiral_restr0.060.22706
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113769
LS refinement shellResolution: 3.48→3.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 96 -
Rwork0.254 1873 -
all-1969 -
obs--62.95 %

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