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- PDB-4uuz: MCM2-histone complex -

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Basic information

Entry
Database: PDB / ID: 4uuz
TitleMCM2-histone complex
Components
  • DNA REPLICATION LICENSING FACTOR MCM2
  • HISTONE H3
  • HISTONE H4
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks ...HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / Switching of origins to a post-replicative state / Unwinding of DNA / polytene chromosome / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / regulation of DNA-templated DNA replication initiation / nucleosomal DNA binding / nuclear chromosome / DNA replication origin binding / cochlea development / DNA replication initiation / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / cellular response to interleukin-4 / DNA helicase activity / Assembly of the pre-replicative complex / Orc1 removal from chromatin / structural constituent of chromatin / nucleosome / nucleosome assembly / single-stranded DNA binding / chromosome / histone binding / DNA helicase / chromosome, telomeric region / DNA replication / cilium / protein heterodimerization activity / intracellular membrane-bounded organelle / apoptotic process / chromatin / enzyme binding / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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 domain 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 / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H3 / DNA replication licensing factor MCM2 / Histone H4
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRichet, N. / Liu, D. / Legrand, P. / Bakail, M. / Compper, C. / Besle, A. / Guerois, R. / Ochsenbein, F.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural Insight Into How the Human Helicase Subunit Mcm2 May Act as a Histone Chaperone Together with Asf1 at the Replication Fork.
Authors: Richet, N. / Liu, D. / Legrand, P. / Velours, C. / Corpet, A. / Gaubert, A. / Bakail, M. / Moal-Raisin, G. / Guerois, R. / Compper, C. / Besle, A. / Guichard, B. / Almouzni, G. / Ochsenbein, F.
History
DepositionAug 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Apr 6, 2016Group: Structure summary
Revision 1.3Jul 3, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Other / Source and taxonomy
Category: entity_src_gen / exptl_crystal_grow ...entity_src_gen / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE H3
B: HISTONE H4
C: DNA REPLICATION LICENSING FACTOR MCM2


Theoretical massNumber of molelcules
Total (without water)34,7983
Polymers34,7983
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-44.3 kcal/mol
Surface area11210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.090, 140.090, 65.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein HISTONE H3


Mass: 15421.101 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: P02299
#2: Protein HISTONE H4


Mass: 11408.452 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: P84040
#3: Protein DNA REPLICATION LICENSING FACTOR MCM2 / MCM2 / MINICHROMOSOME MAINTENANCE PROTEIN 2 HOMOLOG / NUCLEAR PROTEIN BM28


Mass: 7968.699 Da / Num. of mol.: 1 / Fragment: RESIDUES 69-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ) / Variant (production host): GOLD / References: UniProt: P49736, DNA helicase
Sequence detailsFRAGMENT FROM AMINO-ACID 69 TO 138

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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 % sol: 46.7 %
Description: SULFUR ATOM POSITIONS WERE CONFIRMED BY ANALYZING THE ANOMALOUS DIFFERENCE FOURIER MAPS CALCULATED WITH THE PROGRAM ANODE.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES PH7, 21% PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.65312
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2014 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.65312 Å / Relative weight: 1
ReflectionResolution: 2.9→60 Å / Num. obs: 5602 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 159.78 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.7
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KX5

1kx5


Resolution: 2.9→57.89 Å / Cor.coef. Fo:Fc: 0.9502 / Cor.coef. Fo:Fc free: 0.9298 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.355
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 279 4.98 %RANDOM
obs0.199 5602 100 %-
Displacement parametersBiso mean: 131.95 Å2
Baniso -1Baniso -2Baniso -3
1-12.8731 Å20 Å20 Å2
2--12.8731 Å20 Å2
3----25.7461 Å2
Refine analyzeLuzzati coordinate error obs: 0.716 Å
Refinement stepCycle: LAST / Resolution: 2.9→57.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 0 0 1682
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011698HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.152278HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d647SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes247HARMONIC5
X-RAY DIFFRACTIONt_it1698HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion18.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion222SEMIHARMONIC5
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_contact1946SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3508 79 5.04 %
Rwork0.2538 1489 -
all0.2588 1568 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.2112-0.49540.07769.85361.29290.68060.5268-0.1620.01430.0308-1.02050.75440.0879-0.18980.4937-0.1556-0.0115-0.05410.0485-0.1074-0.2397-9.397824.529918.1332
29.97420.7041-0.608810.34341.15251.02840.46410.02420.1088-0.1223-0.9972-0.0481-0.21760.01550.5331-0.11020.0215-0.04860.0499-0.0413-0.2342-5.155723.771116.2726
33.8739-0.9628-0.88176.34831.15972.83020.1841-0.23080.45960.2555-0.4764-0.32860.1995-0.23680.2923-0.0019-0.0158-0.1930.02170.0463-0.041-0.512618.933917.655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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