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

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Basic information

Entry
Database: PDB / ID: 5bnx
TitleCrystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.3-H4 dimer
Components
  • DNA replication licensing factor MCM2
  • Histone H3.3H3F3A
  • Histone H4
  • Histone chaperone ASF1B
KeywordsCHAPERONE/DNA BINDING PROTEIN / DNA replication / MCM2 / ASF1 / H3.3-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 / blastocyst hatching / 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 ...Switching of origins to a post-replicative state / Unwinding of DNA / histone chaperone activity / blastocyst hatching / 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 / nucleosomal DNA binding / regulation of DNA-templated DNA replication initiation / cochlea development / DNA unwinding involved in DNA replication / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / 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 / Activation of ATR in response to replication stress / 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 / 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 / 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 / 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 / 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) / positive regulation of cell growth / spermatogenesis / Oxidative Stress Induced Senescence / DNA helicase / Estrogen-dependent gene expression / DNA replication / chromosome, telomeric region / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / apoptotic process / chromatin / enzyme binding / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding
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 H3.3 / Histone chaperone ASF1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 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

Downloads & links

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Assembly

Deposited unit
A: Histone H3.3
B: Histone H4
C: DNA replication licensing factor MCM2
D: Histone chaperone ASF1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1575
Polymers46,0654
Non-polymers921
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-59 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.519, 110.519, 95.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Histone H3.3 / H3F3A


Mass: 9026.496 Da / Num. of mol.: 1 / Fragment: UNP residues 58-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243
#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

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Non-polymers , 2 types, 125 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.32 %
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-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2013
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 29872 / % possible obs: 99.3 % / Redundancy: 11.9 % / Net I/σ(I): 29.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.4 % / % possible all: 98.4

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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: 2.305→47.818 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 1513 5.08 %Random selection
Rwork0.1841 ---
obs0.1857 29778 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.305→47.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 6 124 3090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083017
X-RAY DIFFRACTIONf_angle_d1.2544079
X-RAY DIFFRACTIONf_dihedral_angle_d16.1651136
X-RAY DIFFRACTIONf_chiral_restr0.091456
X-RAY DIFFRACTIONf_plane_restr0.006538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3054-2.37980.31231400.26882458X-RAY DIFFRACTION96
2.3798-2.46480.28471400.24092519X-RAY DIFFRACTION98
2.4648-2.56350.29741210.22852572X-RAY DIFFRACTION99
2.5635-2.68020.22821310.21762512X-RAY DIFFRACTION99
2.6802-2.82140.31471360.212555X-RAY DIFFRACTION99
2.8214-2.99820.21531310.19732541X-RAY DIFFRACTION99
2.9982-3.22960.23791580.18692554X-RAY DIFFRACTION100
3.2296-3.55460.21311310.16592614X-RAY DIFFRACTION99
3.5546-4.06870.20651490.15832572X-RAY DIFFRACTION100
4.0687-5.12520.16961350.15092631X-RAY DIFFRACTION100
5.1252-47.82840.1841410.19642737X-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)
18.9370.21754.13433.4549-1.48354.0970.1172-0.0143-0.3214-0.0341-0.1194-0.36660.40160.5306-0.05560.54880.01650.03690.3857-0.04380.1553-35.461513.8872-11.8785
23.5687-2.65091.86867.4846-2.93934.3135-0.125-0.23030.50390.4460.1360.1323-0.68230.167-0.04480.5032-0.14890.07620.3293-0.07590.3326-46.313831.1122-14.8364
32.7044.87680.67969.91874.15557.08110.25550.05590.11190.28690.3552-0.3606-0.90951.1291-0.54820.6385-0.14480.09860.4238-0.05490.301-38.90637.2853-17.8839
46.14593.00992.68815.54864.0134.17090.14690.2798-0.6039-1.23050.737-1.6825-0.15940.6717-0.71420.54190.0130.01730.31540.02040.2759-41.68262.8369-27.3751
57.9174-0.5386-1.38522.29011.88459.77920.07030.13150.0997-0.7260.0990.8158-0.4416-0.7808-0.11450.4172-0.03240.02430.1753-0.00940.2951-51.967225.858-19.9974
66.7167-1.39234.61784.7313-2.52075.40880.385-0.20360.13810.436-0.3902-0.7978-0.13210.87450.12250.482-0.14570.0220.5962-0.04490.3713-31.377723.0758-9.0308
75.6111-5.7954-6.46025.96416.66937.3695-0.2046-0.98880.17210.63780.49820.00090.9502-0.41830.02560.5417-0.17030.02830.5762-0.03460.3239-43.241740.0792-2.475
85.1737-3.37932.87419.5456-6.65574.7199-0.44950.5916-0.2012-1.50110.94871.07140.5032-1.8227-0.59610.72520.027-0.14580.68150.02950.3785-58.224922.5177-23.3791
92.7687-1.29942.2626.4361-0.96635.27360.2944-0.1511-0.2227-0.1639-0.228-0.14160.55940.2459-0.06640.52640.01310.05650.37630.01050.1828-42.74397.0815-10.252
106.3987-1.0382-2.91757.27940.99981.28830.6422-0.0537-0.01791.21530.0507-0.56480.00331.0825-0.78860.7341-0.1615-0.3580.9436-0.03320.8298-21.543424.7765-0.0558
113.8225-0.8862-0.15552.9831-1.17835.30790.2655-0.6044-0.2610.0826-0.38840.37410.290.46910.43790.4496-0.13960.02590.4343-0.0495-0.0656-38.535547.6272.3189
123.79440.43932.03560.8598-0.31528.28050.1427-0.41480.2482-0.08840.04670.0539-0.2083-0.452-0.17970.3302-0.03210.04410.2831-0.02360.2186-37.822855.4788-5.3065
134.01051.27781.47481.57051.65522.7440.0620.4487-0.1436-0.11080.0656-0.04420.44820.9554-0.31210.4119-0.03670.00950.39320.01420.2311-31.043849.479-14.7102
142.19730.56640.46351.01540.57958.44380.1773-0.03190.0335-0.14230.1115-0.027-0.38580.4002-0.16630.2549-0.05150.01730.35470.00980.1923-34.638252.2147-11.0828
155.0674-0.22030.61742.7649-2.39783.6950.59410.5978-0.0628-0.4403-0.19660.22961.10240.457-0.34980.5154-0.04140.00780.2716-0.02460.2393-40.073247.1404-13.4199
163.7046-2.0893-0.68813.62092.43832.6052-0.2971.6911-0.8213-1.5005-0.33912.3809-1.1-3.64880.21980.76720.1038-0.19561.4560.16320.6625-53.935956.2366-32.609
171.9054-0.97942.72424.5861-1.71955.83780.12040.73450.3424-0.63020.25660.6007-0.5398-1.5484-0.24140.4797-0.0255-0.0670.7010.08440.2584-45.017455.927-28.973
183.8896-3.14084.61728.8362-3.40537.38420.3992-0.9483-0.96190.4549-0.0379-0.05480.9202-0.339-0.220.47160.03940.10870.49240.00650.1858-36.848741.5883-2.8596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 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 93 )
7X-RAY DIFFRACTION7chain 'B' and (resid 94 through 102 )
8X-RAY DIFFRACTION8chain 'C' and (resid 68 through 81 )
9X-RAY DIFFRACTION9chain 'C' and (resid 82 through 98 )
10X-RAY DIFFRACTION10chain 'C' and (resid 99 through 124 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 11 )
12X-RAY DIFFRACTION12chain 'D' and (resid 12 through 37 )
13X-RAY DIFFRACTION13chain 'D' and (resid 38 through 62 )
14X-RAY DIFFRACTION14chain 'D' and (resid 63 through 103 )
15X-RAY DIFFRACTION15chain 'D' and (resid 104 through 117 )
16X-RAY DIFFRACTION16chain 'D' and (resid 118 through 124 )
17X-RAY DIFFRACTION17chain 'D' and (resid 125 through 139 )
18X-RAY DIFFRACTION18chain 'D' and (resid 140 through 154 )

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