[English] 日本語
Yorodumi
- PDB-7l4n: Crystal structure of the DRM2 (C397R)-CCG DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l4n
TitleCrystal structure of the DRM2 (C397R)-CCG DNA complex
Components
  • DNA (5'-D(*AP*TP*TP*CP*CP*TP*AP*AP*TP*(C49)P*CP*GP*AP*AP*TP*TP*TP*A)-3')
  • DNA (5'-D(*TP*AP*AP*AP*TP*TP*CP*GP*GP*AP*TP*TP*AP*GP*GP*AP*AP*T)-3')
  • DNA (cytosine-5)-methyltransferase DRM2
KeywordsDNA BINDING PROTEIN/DNA / DNA methyltransferase / complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / defense response to fungus / methylation / DNA binding / nucleoplasm / nucleus
Similarity search - Function
SAM-dependent methyltransferase DRM / SAM-dependent methyltransferase DRM-type domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA (cytosine-5)-methyltransferase DRM2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.247 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: Sci Adv / Year: 2021
Title: Substrate deformation regulates DRM2-mediated DNA methylation in plants.
Authors: Fang, J. / Leichter, S.M. / Jiang, J. / Biswal, M. / Lu, J. / Zhang, Z.M. / Ren, W. / Zhai, J. / Cui, Q. / Zhong, X. / Song, J.
History
DepositionDec 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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 DRM2
B: DNA (5'-D(*TP*AP*AP*AP*TP*TP*CP*GP*GP*AP*TP*TP*AP*GP*GP*AP*AP*T)-3')
C: DNA (5'-D(*AP*TP*TP*CP*CP*TP*AP*AP*TP*(C49)P*CP*GP*AP*AP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2455
Polymers51,7693
Non-polymers4772
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-33 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.292, 231.692, 54.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA (cytosine-5)-methyltransferase DRM2 / Protein DOMAINS REARRANGED METHYLASE 2


Mass: 40676.547 Da / Num. of mol.: 1 / Mutation: C397R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DRM2, At5g14620/At5g14630, T15N1.110/T15N1.120 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9M548, DNA (cytosine-5-)-methyltransferase

-
DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*TP*AP*AP*AP*TP*TP*CP*GP*GP*AP*TP*TP*AP*GP*GP*AP*AP*T)-3')


Mass: 5578.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(*AP*TP*TP*CP*CP*TP*AP*AP*TP*(C49)P*CP*GP*AP*AP*TP*TP*TP*A)-3')


Mass: 5513.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)

-
Non-polymers , 3 types, 345 molecules

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


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#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.: 343 / 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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2% v/v Tacsimate(pH 6.0), 0.1 M BIS-TRIS (pH 6.5) and 20% w/v Polyethylene glycol 3,350.
PH range: 6.0-7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.247→50 Å / Num. obs: 35193 / % possible obs: 97.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.06 / Rrim(I) all: 0.166 / Χ2: 0.499 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.336.81.61934820.4430.6431.7540.41698.4
2.33-2.427.11.24235170.5540.4821.3390.42298.9
2.42-2.537.10.91635070.6920.3590.9880.42598.9
2.53-2.677.10.735440.8180.2720.7540.43599
2.67-2.837.50.49835330.9050.1880.5350.44898.6
2.83-3.057.20.31935040.9530.1240.3440.45398
3.05-3.367.40.16935190.9880.0640.1810.48997.7
3.36-3.857.50.10534980.9940.040.1130.57196.8
3.85-4.857.40.06935080.9960.0260.0750.64396
4.85-507.30.05335810.9980.020.0570.67293.9

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ONJ

4onj


Resolution: 2.247→49.202 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 1994 5.68 %
Rwork0.18 33105 -
obs0.1817 35099 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.03 Å2 / Biso mean: 47.1145 Å2 / Biso min: 22.79 Å2
Refinement stepCycle: final / Resolution: 2.247→49.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 733 32 343 3918
Biso mean--36.52 49.03 -
Num. residues----388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.247-2.30340.34191300.3186217391
2.3034-2.36570.30141450.2835239298
2.3657-2.43530.25451400.261233399
2.4353-2.51390.31271450.2429239999
2.5139-2.60370.25251440.2388238999
2.6037-2.7080.27171440.237239299
2.708-2.83120.25651430.2177237199
2.8312-2.98050.25931420.2177236398
2.9805-3.16720.26721440.2012238098
3.1672-3.41170.19591430.169237497
3.4117-3.75490.1871410.1608234697
3.7549-4.29790.18191440.1396237296
4.2979-5.41390.15651440.1347239596
5.4139-49.2020.16111450.1502242693
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)
11.6949-0.184-0.4682.7346-0.06952.41440.13960.0122-0.28130.1786-0.20570.10590.40920.14680.01070.4911-0.02710.00040.30260.03330.398312.012621.1697-6.037
20.30610.03610.13591.3581-0.55461.0588-0.03040.02220.0330.1714-0.03010.05260.3204-0.07230.07780.3668-0.0091-0.01160.29050.00610.293313.784730.61416.2627
30.9399-0.0401-0.5470.19310.0511.89640.00220.0384-0.0609-0.0782-0.0209-0.0010.15340.03670.00010.30860.0310.00890.28690.01640.274318.649230.1068-11.461
41.66910.14-0.8861.57080.62992.6842-0.05080.1257-0.308-0.12590.0381-0.37140.50210.664-0.01820.43870.12620.03830.64350.06580.48139.604426.823-28.2361
50.8958-0.2597-0.01810.49120.39091.38090.00030.1110.1167-0.07670.0181-0.0226-0.13530.0697-0.01940.31690.00910.00580.27550.02530.271717.009344.3735-9.6989
61.2378-1.0169-0.3882.00260.22181.5125-0.1221-0.20620.07210.20960.0532-0.03860.07510.09320.03370.2689-0.0192-0.01110.2988-0.00120.274518.012144.10088.0909
73.9350.75490.80141.701-0.58592.4453-0.0357-0.348-0.41340.0805-0.1898-0.40450.02380.04680.10660.4385-0.0490.05910.4450.06090.474338.940852.886-12.6006
82.2568-0.4434-0.55013.0051-1.00243.58820.42280.0072-0.4665-1.2136-0.7757-0.1230.73050.38840.16170.61350.16430.00790.41840.02530.57737.247625.2816-6.7186
92.3841.4459-2.22735.97682.23048.5734-0.73180.2037-0.7421-0.2996-1.07810.40660.41940.56480.66671.4910.2174-0.29350.6857-0.07371.705934.11932.8986-8.9207
103.77070.2561-0.40683.26720.02730.72230.8626-0.6408-0.30720.9746-1.092-0.29970.2951.2131-0.07911.18830.1023-0.11830.63420.28211.49838.98297.7261-3.4764
111.27070.7171-0.05232.7138-2.14051.75560.215-0.152-0.2134-0.1143-0.5094-0.7153-0.18260.39120.22430.35020.0390.06510.44250.10330.465438.597237.7877-9.8214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 276 through 295 )A276 - 295
2X-RAY DIFFRACTION2chain 'A' and (resid 296 through 320 )A296 - 320
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 400 )A321 - 400
4X-RAY DIFFRACTION4chain 'A' and (resid 401 through 434 )A401 - 434
5X-RAY DIFFRACTION5chain 'A' and (resid 435 through 547 )A435 - 547
6X-RAY DIFFRACTION6chain 'A' and (resid 548 through 626 )A548 - 626
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 5 )B1 - 5
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 15 )B6 - 15
9X-RAY DIFFRACTION9chain 'B' and (resid 16 through 18 )B16 - 18
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 5 )C1 - 5
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 18 )C6 - 18

+
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