[English] 日本語
Yorodumi
- PDB-7ubu: Crystal structure of ZMET2 in complex with hemimethylated CAG DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ubu
TitleCrystal structure of ZMET2 in complex with hemimethylated CAG DNA and a histone H3Kc9me2 peptide
Components
  • 5MC SSDNA
  • C49 SSDNA
  • DNA (cytosine-5)-methyltransferase 1
  • Histone H3.2
KeywordsTRANSFERASE/DNA / DNA methyltransferase / complex / DNA BINDING PROTEIN / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


chromocenter / DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / negative regulation of gene expression via chromosomal CpG island methylation / structural constituent of chromatin / nucleosome / methylation / protein heterodimerization activity ...chromocenter / DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / negative regulation of gene expression via chromosomal CpG island methylation / structural constituent of chromatin / nucleosome / methylation / protein heterodimerization activity / chromatin binding / DNA binding / nucleus
Similarity search - Function
: / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Bromo adjacent homology domain ...: / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Histone H3.2 / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsFang, J. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119721 United States
CitationJournal: Nat Commun / Year: 2022
Title: Mechanistic basis for maintenance of CHG DNA methylation in plants.
Authors: Fang, J. / Jiang, J. / Leichter, S.M. / Liu, J. / Biswal, M. / Khudaverdyan, N. / Zhong, X. / Song, J.
History
DepositionMar 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 1
P: Histone H3.2
B: 5MC SSDNA
C: C49 SSDNA
Q: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9716
Polymers105,5865
Non-polymers3841
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-37 kcal/mol
Surface area35870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.574, 121.392, 160.446
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA chain , 2 types, 2 molecules BC

#3: DNA chain 5MC SSDNA


Mass: 5583.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)
#4: DNA chain C49 SSDNA


Mass: 5537.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)

-
Protein / Protein/peptide , 2 types, 3 molecules APQ

#1: Protein DNA (cytosine-5)-methyltransferase 1 / Chromomethylase 1 / DNA cytosine methyltransferase MET2a / Zea methyltransferase2 / Zmet2


Mass: 87504.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: MET2A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9AXT8, DNA (cytosine-5-)-methyltransferase
#2: Protein/peptide Histone H3.2


Mass: 3480.077 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: H3C2, H3C3, H3C4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P69246

-
Non-polymers , 2 types, 121 molecules

#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 15% w/v polyethylene glycol 6,000
PH range: 5.0-7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.39→160.45 Å / Num. obs: 50383 / % possible obs: 99.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 62.9 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.062 / Rrim(I) all: 0.143 / Net I/σ(I): 10.1 / Num. measured all: 286070
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.39-2.4761.8732754246040.380.842.0580.899.9
9.56-160.4550.03645499050.9970.0180.0432.798.9

-
Processing

Software
NameVersionClassification
HKL-30000.5.32data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FT2

4ft2


Resolution: 2.39→96.81 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 2000 3.98 %
Rwork0.2114 48221 -
obs0.2132 50221 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.33 Å2 / Biso mean: 77.662 Å2 / Biso min: 40.09 Å2
Refinement stepCycle: final / Resolution: 2.39→96.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5803 733 26 120 6682
Biso mean--64.89 67.98 -
Num. residues----776
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.450.38921390.3873342348198
2.45-2.520.41411420.37253423356599
2.52-2.590.38191420.34723436357899
2.59-2.670.3761410.327533983539100
2.67-2.770.35221420.311434203562100
2.77-2.880.32191430.296934363579100
2.88-3.010.31591410.28993414355599
3.01-3.170.31081420.26443429357199
3.17-3.370.32721430.23573441358499
3.37-3.630.23981420.22043430357299
3.63-3.990.24381430.19933425356898
3.99-4.570.20821430.15323468361198
4.57-5.760.20041450.15863495364098
5.76-96.810.2091520.173664381698
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)
13.07111.9350.05368.8844-0.70161.3376-0.041-0.01050.0250.15190.0478-0.3473-0.15810.1267-0.00850.35890.00970.00270.53990.03740.5552-2.258923.078412.5213
21.61320.5305-0.06812.63740.66210.8926-0.070.1808-0.4855-0.14110.00170.04040.19720.00730.07160.40220.02540.00320.40470.02540.5743-28.619-15.10150.4167
31.37340.3924-0.48561.5016-0.33461.09110.0508-0.2069-0.11060.2739-0.0550.14040.0368-0.035-0.00150.4673-0.0099-0.00440.48160.05880.6211-40.8051-0.554222.4789
44.2003-1.5836-3.94734.41630.72753.9726-0.1477-0.2848-0.53110.5793-0.48680.347-0.05370.39850.3690.9598-0.0168-0.18171.1705-0.13291.17156.68521.488324.2743
56.0315-5.1442-5.53524.38314.71875.07180.797-0.65381.84030.3947-1.11441.3851-1.0859-1.07320.19640.67030.02340.07110.7414-0.04621.1527-8.346621.108221.748
67.3862-6.0372-7.01955.77265.69756.6738-0.7371-0.05351.13410.63031.3731-2.3053-0.39281.1295-0.06421.0152-0.1445-0.04140.9661-0.14791.497-29.209821.201323.0136
71.94652.64161.90427.2273.66292.17810.77370.95332.42150.6744-0.97550.6194-1.86260.02920.12410.90090.08660.15910.96760.1321.1669-39.632520.361525.8805
82.95590.74711.3275.6094-0.78160.8463-0.1712-0.1442-0.8626-0.2796-0.1114-0.34170.93950.026-0.01651.2853-0.03580.16030.99530.13841.0057-41.1558-26.404333.9634
93.71911.3593-2.72133.8698-1.4282.03820.3218-1.378-0.43030.7476-0.6562-0.57140.00310.37430.27830.8703-0.054-0.10720.90040.16450.7413-32.1061-8.443440.4112
106.25343.87990.07177.19960.36518.98850.2258-0.11922.70721.335-0.6231-0.2729-1.1603-0.85540.340.95030.02330.00150.8008-0.1381.1429-29.335612.24337.0108
115.13374.0816-5.42925.4534-3.97595.7914-2.1622-0.3376-0.7460.06780.6655-0.46961.1212-1.09951.83961.37330.0193-0.25891.3708-0.78131.8683-31.363720.906447.8104
126.74042.3181.56543.88273.7593.54710.8031-0.45170.63730.7608-0.0379-1.4623-0.251-0.1524-0.81690.9255-0.0787-0.08070.6967-0.02571.0045-30.12897.452638.5416
135.45594.8055-4.48668.0438-6.40627.3872-0.2323-0.5047-0.87450.6442-0.0971-0.01480.91040.03570.29191.0666-0.0295-0.00420.81730.27291.0139-36.7565-22.598638.7578
142.3561-0.446-3.55390.15570.81425.77570.65230.337-0.0481-0.0641-0.1141-0.07860.18910.4414-0.52230.9565-0.0020.02440.8987-0.17411.1948-32.1549-41.6378-8.574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 133 through 268 )A133 - 268
2X-RAY DIFFRACTION2chain 'A' and (resid 269 through 518 )A269 - 518
3X-RAY DIFFRACTION3chain 'A' and (resid 519 through 889 )A519 - 889
4X-RAY DIFFRACTION4chain 'P' and (resid 2 through 6 )P2 - 6
5X-RAY DIFFRACTION5chain 'P' and (resid 7 through 14 )P7 - 14
6X-RAY DIFFRACTION6chain 'P' and (resid 15 through 19 )P15 - 19
7X-RAY DIFFRACTION7chain 'P' and (resid 20 through 24 )P20 - 24
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 5 )B1 - 5
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 11 )B6 - 11
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 16 )B12 - 16
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 18 )B17 - 18
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 11 )C1 - 11
13X-RAY DIFFRACTION13chain 'C' and (resid 12 through 18 )C12 - 18
14X-RAY DIFFRACTION14chain 'Q' and (resid 0 through 11 )Q0 - 11

+
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