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- PDB-5bnv: Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 t... -

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Basic information

Entry
Database: PDB / ID: 5bnv
TitleCrystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer
Components
  • DNA replication licensing factor MCM2
  • Histone H3.3H3F3A
  • Histone H4
KeywordsCHAPERONE/DNA BINDING PROTEIN / DNA replication / MCM2 helicase / histone chaperone / H3-H4 tetramer / CHAPERONE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / 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 ...Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / 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 / Oxidative Stress Induced Senescence / DNA helicase / Estrogen-dependent gene expression / DNA replication / chromosome, telomeric region / 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 / membrane / metal ion binding / nucleus / cytoplasm
Similarity search - Function
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 ...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 / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DNA replication licensing factor MCM2 / Histone H4 / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 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 1.4Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Mar 10, 2021Group: Data collection / Category: reflns / Item: _reflns.observed_criterion
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 H3.3
B: Histone H4
D: Histone H3.3
E: Histone H4
F: DNA replication licensing factor MCM2
C: DNA replication licensing factor MCM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5859
Polymers56,3006
Non-polymers2853
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17440 Å2
ΔGint-120 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.592, 110.592, 203.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Histone H3.3 / H3F3A


Mass: 9026.496 Da / Num. of mol.: 2 / 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 / Plasmid: pETduet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIL / References: UniProt: P84243
#2: Protein Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 2
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: pETduet / 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.: 2 / 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 / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / References: UniProt: P49736
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 5.55 Å3/Da / Density % sol: 81.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5 M sodium/potassium phosphate, pH 8.0 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.795→97.144 Å / Num. all: 32022 / Num. obs: 31946 / % possible obs: 100 % / Redundancy: 14.1 % / Net I/σ(I): 29.7
Reflection shellResolution: 2.795→2.95 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.795→48.056 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1597 5 %Random selection
Rwork0.196 ---
obs0.1974 31936 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.795→48.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 15 31 3313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083307
X-RAY DIFFRACTIONf_angle_d1.2124440
X-RAY DIFFRACTIONf_dihedral_angle_d15.6461274
X-RAY DIFFRACTIONf_chiral_restr0.089506
X-RAY DIFFRACTIONf_plane_restr0.005581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7951-2.88530.35411390.34152651X-RAY DIFFRACTION98
2.8853-2.98840.33741440.28312722X-RAY DIFFRACTION100
2.9884-3.1080.28381410.2742693X-RAY DIFFRACTION100
3.108-3.24940.30321440.26552728X-RAY DIFFRACTION100
3.2494-3.42070.3091420.24052711X-RAY DIFFRACTION100
3.4207-3.63490.23711450.2022744X-RAY DIFFRACTION100
3.6349-3.91550.20011450.1732744X-RAY DIFFRACTION100
3.9155-4.30930.19511450.15692758X-RAY DIFFRACTION100
4.3093-4.93230.16881470.13672787X-RAY DIFFRACTION100
4.9323-6.21210.18691480.19212819X-RAY DIFFRACTION100
6.2121-48.06320.20331570.19592982X-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)
13.53634.14520.10046.5104-3.33826.63390.4683-1.65170.67330.2950.20990.1958-0.24540.4905-0.54750.49490.0694-0.06190.6681-0.10380.291110.468527.089314.3978
26.8106-5.9734-0.72955.53731.74445.65830.0147-1.04170.47170.7712-0.14810.1247-0.6235-1.4613-0.0171.00260.05470.19631.70110.1770.7537-1.924423.585321.4825
35.68542.6805-3.58486.0628-4.02673.9164-0.2054-0.3344-0.1881-0.3786-0.0884-0.22940.67760.15440.27340.29060.0128-0.01020.3549-0.02120.30169.173824.8551-1.0614
44.51241.9613-4.73853.3223-3.46595.7920.058-0.17821.3285-0.76620.520.627-1.30111.3337-0.48340.54750.0129-0.07230.5227-0.07410.429313.489336.959-12.7233
52.18186.22582.6974.0421.9862.5203-0.2835-0.30950.72270.12250.15310.425-0.2166-0.9450.10720.43660.0243-0.06720.5369-0.0440.48791.359831.8694-7.4467
63.9341-1.0453-3.25333.14544.03976.2058-0.0353-1.3332-0.27111.2492-0.27320.55541.0652-0.28110.47231.2241-0.04350.08460.7451-0.16050.772117.594336.251224.2263
76.20951.31480.62324.4794.44674.5166-0.3842-0.29170.370.05490.1222-0.0836-0.29690.51150.31710.50610.1008-0.0430.4206-0.01080.328316.811532.16261.5225
87.42034.5405-2.70978.9982-5.56995.45640.3495-0.4520.16680.42030.23231.4996-0.3673-0.8724-0.5530.39970.03730.0050.8014-0.03030.5426-0.910522.846410.2428
90.2836-0.67280.20383.2533-2.67752.54450.6472-2.33961.7424-0.9125-0.44220.38761.1188-3.05-0.32121.1819-0.2102-0.79581.1270.04881.53950.671817.42831.3659
105.0281-3.78654.59083.1743-3.04484.6566-0.033-1.8968-0.7125-0.45010.37410.2726-0.5951-2.1795-0.14860.5926-0.1008-0.17170.74980.1130.4992-20.185723.5082-28.3072
113.6144-5.09055.07377.9265-6.42539.88050.91590.6355-1.6558-0.9325-1.04150.99871.35010.5126-0.06350.7541-0.1208-0.11260.4899-0.03150.9856-14.73477.682-29.616
129.9901-8.1755-6.66086.74355.51854.5099-0.19590.9759-2.9376-1.3931-0.32732.72960.8732-0.80660.49041.3482-0.2645-0.42130.83580.15121.5241-19.1891-0.6509-25.1913
139.55244.08743.04114.72251.19011.58690.5537-0.9146-0.23580.5202-0.43030.3120.094-0.3315-0.07440.5246-0.0776-0.07950.4990.13550.2999-9.585623.5759-19.991
144.55160.48084.69094.2433-2.8287.3444-1.38341.07581.8168-3.06180.2052-0.1688-1.52930.40511.22430.7876-0.1256-0.19840.55720.13640.45092.200435.253-25.5433
153.19135.1948-1.04028.0829-1.50662.1680.376-0.0617-0.68871.1586-0.1427-0.56720.59020.743-0.39990.66850.0507-0.15420.49420.12340.42763.574524.4875-19.5304
164.12823.9748-1.11844.2425-0.17672.4940.49411.0618-1.984-0.71380.4756-1.56450.2460.5964-0.6610.75320.0048-0.11780.70280.02781.07131.231518.4956-15.6998
179.7153-0.14081.88128.8742-3.69944.5786-0.53690.79410.1328-0.48430.1977-0.1689-0.1582-0.00850.21260.4781-0.0645-0.05890.530.08730.2798-9.4926.9713-30.2483
185.97273.3177-0.47629.4932-3.34255.0441-0.0403-0.7174-1.74590.41970.3401-0.02910.5115-0.3346-0.16380.6162-0.0012-0.12260.64640.35390.8992-11.13768.1878-19.4069
191.6928-2.2334-0.82049.0212-2.20112.207-0.3151.91832.0676-1.2951-0.0433-1.4613-1.40020.30370.53790.9547-0.1953-0.11640.85470.21930.787-7.271436.5109-34.9126
203.4127-1.0277-3.34544.9947-0.00783.62641.08720.43540.9185-1.14091.341-0.1159-0.12730.49380.04910.6304-0.0424-0.14820.37060.09480.6544-17.135932.4664-35.8179
214.0677-1.1273-2.93014.0587-2.43485.2366-0.83971.2181-1.4982-1.33490.71920.8029-0.095-0.2745-0.23970.6769-0.1079-0.26180.6262-0.00370.5883-24.149621.9653-37.6911
229.62360.95280.62532.0149-2.26918.0611-0.62450.5818-1.8719-0.8510.0309-0.56241.175-0.05010.22550.8842-0.2499-0.03910.68370.12210.9716-25.10838.4614-30.3588
231.5937-2.05051.83175.5174-5.54375.3140.0628-0.8063-0.496-1.1997-0.1774-0.50451.17860.8871-0.27841.2796-0.0685-0.07791.68690.53111.7777-27.2754-0.9006-14.8694
248.72272.4869-1.81822.26960.19432.9478-0.9798-0.098-0.97180.89361.35740.86730.7831-1.0322-0.6951.05220.0014-0.10551.30950.81871.5748-6.4871-0.8892-8.9547
252.85061.2585-2.34672.1903-1.47252.09830.48040.99141.66370.3381-0.30930.4354-0.94810.4503-0.38130.7457-0.0860.01020.4842-0.03440.709523.925137.2021-4.6118
263.26213.2061-1.34015.0737-1.37213.8690.6897-1.04080.07791.1268-0.1157-0.0812-0.3192-0.1904-0.43840.788-0.0181-0.10440.88140.00760.368319.522727.015515.1706
274.8094-0.49184.6562.3233-0.32034.20442.5167-4.2454-0.02482.48410.1039-0.57610.9241-0.3407-2.17111.8598-0.2184-0.06581.8419-0.02941.0177-0.70698.369322.9862
288.3127-0.3273-0.70949.3204-4.34968.14940.38390.4464-0.30240.32180.26151.2144-0.8638-1.6582-0.6310.95220.02750.11.3610.27841.2407-14.360116.68578.7399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 114 )
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 120 )
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 134 )
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 25 )
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 47 )
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 92 )
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 97 )
10X-RAY DIFFRACTION10chain 'D' and (resid 58 through 63 )
11X-RAY DIFFRACTION11chain 'D' and (resid 64 through 78 )
12X-RAY DIFFRACTION12chain 'D' and (resid 79 through 85 )
13X-RAY DIFFRACTION13chain 'D' and (resid 86 through 114 )
14X-RAY DIFFRACTION14chain 'D' and (resid 115 through 120 )
15X-RAY DIFFRACTION15chain 'D' and (resid 121 through 130 )
16X-RAY DIFFRACTION16chain 'D' and (resid 131 through 135 )
17X-RAY DIFFRACTION17chain 'E' and (resid 26 through 47 )
18X-RAY DIFFRACTION18chain 'E' and (resid 48 through 94 )
19X-RAY DIFFRACTION19chain 'F' and (resid 68 through 76 )
20X-RAY DIFFRACTION20chain 'F' and (resid 77 through 81 )
21X-RAY DIFFRACTION21chain 'F' and (resid 82 through 87 )
22X-RAY DIFFRACTION22chain 'F' and (resid 88 through 97 )
23X-RAY DIFFRACTION23chain 'F' and (resid 98 through 106 )
24X-RAY DIFFRACTION24chain 'F' and (resid 107 through 125 )
25X-RAY DIFFRACTION25chain 'C' and (resid 68 through 76 )
26X-RAY DIFFRACTION26chain 'C' and (resid 77 through 97 )
27X-RAY DIFFRACTION27chain 'C' and (resid 98 through 106 )
28X-RAY DIFFRACTION28chain 'C' and (resid 107 through 124 )

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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