[English] 日本語
Yorodumi
- PDB-5bnx: Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histo... -

+
Open data


ID or keywords:

Loading...

-
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 H3.3
  • 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 / negative regulation of chromosome condensation / Barr body / : / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / blastocyst hatching / CMG complex ...Switching of origins to a post-replicative state / Unwinding of DNA / histone chaperone activity / negative regulation of chromosome condensation / Barr body / : / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / blastocyst hatching / CMG complex / inner kinetochore / pericentric heterochromatin formation / DNA replication-dependent chromatin assembly / MCM complex / muscle cell differentiation / double-strand break repair via break-induced replication / mitotic DNA replication initiation / oocyte maturation / regulation of DNA-templated DNA replication initiation / nucleosomal DNA binding / nucleus organization / spermatid development / DNA replication origin binding / cochlea development / Activation of the pre-replicative complex / DNA replication initiation / single fertilization / negative regulation of megakaryocyte differentiation / subtelomeric heterochromatin formation / protein localization to CENP-A containing chromatin / Activation of ATR in response to replication stress / RNA polymerase II core promoter sequence-specific DNA binding / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / embryo implantation / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / DNA helicase activity / Assembly of the ORC complex at the origin of replication / cellular response to interleukin-4 / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Assembly of the pre-replicative complex / 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 / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Orc1 removal from chromatin / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / multicellular organism growth / Transcriptional regulation of granulopoiesis / HCMV Early Events / male gonad development / osteoblast differentiation / structural constituent of chromatin / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / single-stranded DNA binding / Processing of DNA double-strand break ends / HATs acetylate histones / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cell growth / Oxidative Stress Induced Senescence / histone binding / spermatogenesis
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 H3.3 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
Protein , 4 types, 4 molecules ABCD

#1: Protein Histone H3.3


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

-
Non-polymers , 2 types, 125 molecules

#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
#6: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 )

+
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