[English] 日本語
Yorodumi
- PDB-5c3i: Crystal structure of the quaternary complex of histone H3-H4 hete... -

+
Open data


ID or keywords:

Loading...

-
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 H3.1
  • Histone H4
  • Histone chaperone ASF1A
KeywordsREPLICATION / histone / chaperone / ASF1 / MCM protein
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Unwinding of DNA / histone chaperone activity / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / DNA replication-dependent chromatin assembly / MCM complex / muscle cell differentiation / double-strand break repair via break-induced replication ...Switching of origins to a post-replicative state / Unwinding of DNA / histone chaperone activity / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / DNA replication-dependent chromatin assembly / MCM complex / muscle cell differentiation / double-strand break repair via break-induced replication / mitotic DNA replication initiation / regulation of DNA-templated DNA replication initiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / replication fork processing / DNA replication origin binding / cochlea development / Activation of the pre-replicative complex / DNA replication initiation / Activation of ATR in response to replication stress / 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 / 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 / cellular response to interleukin-4 / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / DNA helicase activity / epigenetic regulation of gene expression / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / 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 / Negative Regulation of CDH1 Gene Transcription / HDACs deacetylate histones / Assembly of the pre-replicative complex / 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 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / Orc1 removal from chromatin / 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 / site of double-strand break / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA helicase / DNA replication / chromosome, telomeric region / cilium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / intracellular membrane-bounded organelle / DNA repair
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-like, winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / 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-like, winged-helix 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 C-terminal AAA(+) ATPase domain (MCM-CTD) profile. / minichromosome maintenance proteins / MCM domain / Histone, subunit A / Histone, subunit A / 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 / 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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/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
Has protein modificationN
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.

-
Experimental details

-
Experiment

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

-
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

-
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: _

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

-
Phasing

PhasingMethod: molecular replacement

-
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 %

+
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