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- PDB-5bo0: Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histo... -

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Basic information

Entry
Database: PDB / ID: 5bo0
TitleCrystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.2-H4 dimer
Components
  • DNA replication licensing factor MCM2
  • Histone H3.2
  • Histone H4
  • Histone chaperone ASF1B
KeywordsCHAPERONE/DNA BINDING PROTEIN / DNA replication / MCM2 / ASF1b / H3.2-H4 dimer / CHAPERONE-DNA BINDING PROTEIN complex
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 / blastocyst hatching / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / DNA replication-dependent chromatin assembly / MCM complex / 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 / blastocyst hatching / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / DNA replication-dependent chromatin assembly / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / regulation of DNA-templated DNA replication initiation / cochlea development / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Activation of ATR in response to replication stress / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / cellular response to interleukin-4 / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Assembly of the pre-replicative complex / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / 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 / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / Orc1 removal from chromatin / 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 / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / spermatogenesis / DNA helicase / Estrogen-dependent gene expression / histone binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / cell differentiation / chromosome, telomeric region / DNA replication / cilium / Amyloid fiber formation / protein heterodimerization activity / intracellular membrane-bounded organelle / apoptotic process / chromatin / enzyme binding / 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-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 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 / 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 H3.2 / Histone chaperone ASF1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.906 Å
AuthorsHuang, H. / Patel, D.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks.
Authors: Huang, H. / Strmme, C.B. / Saredi, G. / Hodl, M. / Strandsby, A. / Gonzalez-Aguilera, C. / Chen, S. / Groth, A. / Patel, D.J.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Aug 19, 2015Group: Database references
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: DNA replication licensing factor MCM2
D: Histone chaperone ASF1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3635
Polymers46,2704
Non-polymers921
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-58 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.964, 112.964, 98.226
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Histone H3.2 / Histone H3/m / Histone H3/o


Mass: 9231.793 Da / Num. of mol.: 1 / Fragment: UNP residues 57-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST2H3A, HIST2H3C, H3F2, H3FM, HIST2H3D / Production host: Escherichia coli (E. coli) / References: UniProt: Q71DI3
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 1
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 (E. coli) / 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.: 1 / Fragment: UNP residues 61-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2, BM28, CCNL1, CDCL1, KIAA0030 / Production host: Escherichia coli (E. coli) / References: UniProt: P49736
#4: Protein Histone chaperone ASF1B / Anti-silencing function protein 1 homolog B / hAsf1b / CCG1-interacting factor A-II / hCIA-II


Mass: 17915.113 Da / Num. of mol.: 1 / Fragment: UNP residues 1-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVP2
#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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 3.2 M sodium formate, 0.1 M Tris, pH 8.5 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 16336 / % possible obs: 100 % / Redundancy: 10.3 % / Net I/σ(I): 25.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.906→48.915 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 824 5.05 %Random selection
Rwork0.1902 ---
obs0.1926 16311 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.906→48.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 6 0 2970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013021
X-RAY DIFFRACTIONf_angle_d1.3984084
X-RAY DIFFRACTIONf_dihedral_angle_d16.6151139
X-RAY DIFFRACTIONf_chiral_restr0.099457
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9064-3.08850.40051600.34662505X-RAY DIFFRACTION100
3.0885-3.32690.30561310.27122573X-RAY DIFFRACTION100
3.3269-3.66160.32831290.22432545X-RAY DIFFRACTION100
3.6616-4.19120.23871300.17972578X-RAY DIFFRACTION100
4.1912-5.27950.20191320.15162583X-RAY DIFFRACTION100
5.2795-48.92180.19181420.17092703X-RAY DIFFRACTION100
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)
14.01460.06172.63194.1788-0.7341.9525-0.0473-0.0825-0.54780.25570.1671-0.05270.18790.257-0.11130.4298-0.01990.02290.2579-0.12580.178315.3627112.352135.6813
24.3487-1.13520.84832.512-1.38581.6122-0.1035-0.3602-0.47630.20780.4114-0.1483-0.30650.0078-0.10090.5110.03920.03270.2301-0.07910.256415.338121.145239.2306
33.74571.76411.33472.33050.97164.42790.3440.2381-0.1967-0.23310.06940.0083-0.52030.0959-0.24490.8587-0.2130.02830.2540.02750.525111.0442136.154729.7225
41.83921.1080.14457.36253.73082.4160.41590.1578-0.7169-0.79810.1861-1.4005-0.41130.004-0.44280.47040.0869-0.01330.2899-0.04620.640512.9887101.190921.243
53.0116-0.805-0.36523.18011.31353.7519-0.2997-0.1054-0.0282-0.5959-0.12450.7106-0.4782-0.36680.15790.39850.05710.058-0.0962-0.0650.42752.7131123.833830.0249
62.7161-1.06821.20692.7735-1.35963.0678-0.06730.4305-0.288-0.0697-0.1633-1.056-0.58660.9050.07590.4405-0.0862-0.03890.3297-0.07010.510923.5652119.838937.5822
73.44430.90890.57054.4013-1.59734.2824-0.1518-0.46250.7220.4190.2881-0.4461-0.19540.3647-0.170.5359-0.1195-0.05250.4258-0.08890.629123.6565122.626748.6303
83.74320.006-1.24364.2752-0.15671.25290.4682-0.57230.11320.3396-0.2350.21410.0206-0.238-0.06860.5435-0.44610.19350.56-0.19080.908612.0311137.774347.7179
92.4-1.87241.50595.7884-3.07692.4022-0.04140.347-0.742-0.55540.43130.99620.0164-0.9116-0.26410.43990.1658-0.06770.4561-0.01140.6086-2.493117.641827.9975
103.10421.25111.21182.42420.49132.7321-0.0735-0.0446-0.55620.87190.6618-0.5550.36350.4217-0.37030.51060.1291-0.16120.3147-0.09630.691821.0678106.465646.0704
110.0447-0.18210.17871.2505-1.36772.197-0.0397-0.44461.0398-0.26180.1675-0.4077-0.39250.4299-0.16160.7305-0.1278-0.00840.9625-0.12261.997435.545126.937646.3137
124.6265-0.6381-0.11983.7710.69841.47320.3224-0.41430.31570.1147-0.20910.4594-0.0634-0.0915-0.120.38-0.03660.10680.275-0.01210.443416.5688146.597951.3992
130.8223-0.62390.73890.6441-0.77612.1536-0.1941-0.08550.4541-0.12510.2283-0.0412-0.626-0.44630.04770.4112-0.0622-0.04530.23110.03230.556414.0772155.21240.4933
141.3123-0.59410.97110.8960.36344.5982-0.0710.0366-0.2254-0.42860.4574-0.35940.10120.3346-0.04020.6842-0.27720.07740.2190.03150.306626.0416148.241247.8246
154.8771-0.8707-2.37133.98031.88383.4267-0.20740.2381-0.1191-0.22670.0023-0.21450.36430.79480.17991.1011-0.25180.38141.1744-0.02040.257822.2012141.184826.5225
161.8692-0.38410.59050.15280.11051.08260.0941-0.32720.5695-0.57770.41370.1813-0.5492-0.1057-0.30630.478-0.17450.10630.37680.01210.361122.8643153.902547.1893
171.30140.1275-0.35441.8624-0.371.41760.17530.74640.5034-0.57350.1169-0.1636-0.27570.5315-0.12390.687-0.08940.16850.42930.07460.372420.0654147.656831.5158
181.22940.43050.11391.5408-0.76461.4776-0.28560.60480.4686-0.60320.22870.41530.2574-0.1727-0.0010.7443-0.3299-0.07980.15990.40560.282214.932145.015436.5068
192.24081.42190.07044.81413.00172.2395-0.17450.939-0.1291-0.765-0.20010.65640.3443-0.63390.18091.97160.3235-0.63491.30960.04581.03380.577154.181217.9097
200.7127-0.242-0.53831.1735-0.74423.63470.04810.96640.0865-0.42750.19340.3713-0.2088-0.4895-0.07960.9292-0.035-0.34290.69060.48730.93169.7575153.828221.0884
216.7704-3.14562.02213.5613-1.37423.67990.2378-0.2615-0.62330.7228-0.23350.13620.2485-0.1141-0.00370.4364-0.1225-0.00030.23490.06430.670518.4973139.513747.0544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 112 )
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 134 )
4X-RAY DIFFRACTION4chain 'B' and (resid 17 through 30 )
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 47 )
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 82 )
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 93 )
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 102 )
9X-RAY DIFFRACTION9chain 'C' and (resid 68 through 85 )
10X-RAY DIFFRACTION10chain 'C' and (resid 86 through 107 )
11X-RAY DIFFRACTION11chain 'C' and (resid 108 through 124 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 12 )
13X-RAY DIFFRACTION13chain 'D' and (resid 13 through 30 )
14X-RAY DIFFRACTION14chain 'D' and (resid 31 through 44 )
15X-RAY DIFFRACTION15chain 'D' and (resid 45 through 54 )
16X-RAY DIFFRACTION16chain 'D' and (resid 55 through 76 )
17X-RAY DIFFRACTION17chain 'D' and (resid 77 through 103 )
18X-RAY DIFFRACTION18chain 'D' and (resid 104 through 117 )
19X-RAY DIFFRACTION19chain 'D' and (resid 118 through 124 )
20X-RAY DIFFRACTION20chain 'D' and (resid 125 through 139 )
21X-RAY DIFFRACTION21chain 'D' and (resid 140 through 154 )

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