[English] 日本語
Yorodumi
- PDB-7l4f: Crystal structure of the DRM2-CAT DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l4f
TitleCrystal structure of the DRM2-CAT DNA complex
Components
  • DNA (5'-D(*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49)P*AP*TP*CP*CP*TP*TP*TP*A)-3')
  • DNA (5'-D(*TP*AP*AP*AP*GP*GP*AP*TP*GP*AP*GP*GP*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 activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / 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
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / 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: 2.55 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 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id
Revision 2.1Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
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
B: DNA (cytosine-5)-methyltransferase DRM2
C: DNA (5'-D(*TP*AP*AP*AP*GP*GP*AP*TP*GP*AP*GP*GP*AP*GP*GP*AP*AP*T)-3')
D: DNA (5'-D(*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49)P*AP*TP*CP*CP*TP*TP*TP*A)-3')
A: DNA (cytosine-5)-methyltransferase DRM2
E: DNA (5'-D(*TP*AP*AP*AP*GP*GP*AP*TP*GP*AP*GP*GP*AP*GP*GP*AP*AP*T)-3')
G: DNA (5'-D(*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49)P*AP*TP*CP*CP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5349
Polymers103,4346
Non-polymers1,1003
Water97354
1
B: DNA (cytosine-5)-methyltransferase DRM2
C: DNA (5'-D(*TP*AP*AP*AP*GP*GP*AP*TP*GP*AP*GP*GP*AP*GP*GP*AP*AP*T)-3')
D: DNA (5'-D(*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49)P*AP*TP*CP*CP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1014
Polymers51,7173
Non-polymers3841
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-35 kcal/mol
Surface area20210 Å2
MethodPISA
2
A: DNA (cytosine-5)-methyltransferase DRM2
E: DNA (5'-D(*TP*AP*AP*AP*GP*GP*AP*TP*GP*AP*GP*GP*AP*GP*GP*AP*AP*T)-3')
G: DNA (5'-D(*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49)P*AP*TP*CP*CP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4325
Polymers51,7173
Non-polymers7162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-40 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.216, 70.833, 103.735
Angle α, β, γ (deg.)90.000, 98.020, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules BA

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


Mass: 40622.496 Da / Num. of mol.: 2
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, 4 molecules CEDG

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


Mass: 5677.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49)P*AP*TP*CP*CP*TP*TP*TP*A)-3')


Mass: 5416.560 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)

-
Non-polymers , 3 types, 57 molecules

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


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium acetate trihydrate (pH 7.0) and 12% w/v Polyethylene glycol 3,350.
PH range: 6.5-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.55→102.72 Å / Num. obs: 40496 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Net I/σ(I): 14 / Num. measured all: 272465
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
2.55-2.656.71.4763044845680.4130.6151.602199.9
9.19-102.726.30.03858409230.9980.0160.04143.499.5

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ONJ

4onj


Resolution: 2.55→85.267 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 1999 4.94 %
Rwork0.2083 38429 -
obs0.2104 40428 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.07 Å2 / Biso mean: 101.3119 Å2 / Biso min: 48.08 Å2
Refinement stepCycle: final / Resolution: 2.55→85.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 1448 73 54 7017
Biso mean--106.8 79.14 -
Num. residues----771
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.55-2.61380.42051420.36912739100
2.6138-2.68450.34071410.32362701100
2.6845-2.76350.33931400.31052708100
2.7635-2.85270.30441450.30412770100
2.8527-2.95460.32351420.31862744100
2.9546-3.07290.41921420.3232725100
3.0729-3.21280.32091430.2715273799
3.2128-3.38220.29121420.2394271299
3.3822-3.59410.27831430.2339276099
3.5941-3.87160.26521420.2109271799
3.8716-4.26120.21671420.1823274099
4.2612-4.87770.21081440.17242770100
4.8777-6.14520.21861440.1782778100
6.1452-85.2670.20661470.1679282899
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)
10.84150.6014-0.35971.2543-0.12231.34520.0493-0.36350.05880.2653-0.14440.5267-0.0811-0.136100.6247-0.00760.07970.618-0.01040.7786199.2973.76431.296
20.34940.10410.30293.50851.24671.62490.07410.0475-0.067-0.16170.01640.39550.14790.00980.00010.6211-0.0303-0.02410.58620.00870.8348195.232-14.85914.934
32.0591-0.6582-0.07292.93850.19532.1967-0.06320.12990.1811-0.2729-0.00420.2509-0.46860.2144-00.6902-0.1058-0.01220.55240.04590.6583204.41510.59913.848
40.0593-0.0095-0.05860.01250.01630.12080.6978-0.3261.0379-1.68830.7292-0.1334-1.3817-0.24290.0011.43470.06460.33530.87610.00640.9892214.447-15.4480.615
50.1065-0.1888-0.07350.0550.13950.01850.4826-0.27730.04140.38561.0421-0.45891.76410.1669-0.00521.08890.0820.0190.95950.01950.803215.326-19.86721.561
60.4429-0.22250.28260.63950.27470.3010.2743-1.9271-0.20380.61770.02950.49561.31210.0085-0.00191.6915-0.13850.46891.29670.21851.009200.944-18.53440.68
71.53130.81450.6681.14420.61720.3846-0.0232-0.6806-0.07140.33020.15890.15431.02630.5129-0.00081.07610.07580.15880.86180.01220.7669206.575-17.74732.641
80.266-0.0111-0.13270.4421-0.21280.18140.40570.175-0.2205-0.34160.9778-0.65990.35330.4553-0.00221.04190.02130.09471.0462-0.1280.7969219.409-19.8114.486
91.2674-0.2528-0.07840.9979-0.74911.1312-0.25220.1370.557-0.17910.1329-0.3483-0.84641.18420.00151.1367-0.647-0.02551.4635-0.01370.8418234.66624.52326.316
100.55070.5596-0.01820.96740.0860.0394-0.2421-0.4034-0.4334-0.08250.4463-0.35950.31931.5108-0.00050.8295-0.06860.07132.6499-0.24021.0707256.1469.39537.485
113.5970.14620.86762.15060.14114.1683-0.4653-0.09070.23780.16520.3101-0.0499-0.77711.2136-0.00070.9239-0.2996-0.02081.1212-0.08550.6748226.33619.33740.401
120.0240.02150.06360.1644-0.01470.1017-1.0882-0.3297-0.50640.44380.42940.23771.4690.33020.00171.09340.3307-0.19362.0536-0.33171.8452241.704-4.50343.923
130.12820.05380.0090.07010.03250.02410.05540.86440.671-1.21640.22540.62640.97210.2705-0.0011.42220.23670.01392.39790.06471.4213242.6032.32519.73
140.0539-0.00840.03090.02840.0220.04970.57460.18051.15230.65150.5938-0.1796-0.00480.32230.00121.83480.5230.4813.33540.02861.4261255.94710.5459.448
150.14710.152-0.02110.24280.10210.08420.3961-0.5412-0.0333-0.70261.08821.70720.54980.4911-0.00462.08780.04910.16362.98660.36141.1601253.5994.5595.55
160.77250.5398-0.18461.0021-0.77480.74390.11310.2831-0.3055-1.0696-0.6501-0.08410.5082.8923-0.03131.0932-0.16970.08842.534-0.01780.937243.6565.05228.456
170.009-0.0274-0.03120.0598-0.00890.03720.6559-0.0188-0.1658-0.3597-0.0044-0.49020.08830.7452-0.00031.57740.4745-0.16621.7785-0.12041.9232241.637-11.81744.651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 275:341 )B275 - 341
2X-RAY DIFFRACTION2( CHAIN B AND RESID 342:494 )B342 - 494
3X-RAY DIFFRACTION3( CHAIN B AND RESID 495:624 )B495 - 624
4X-RAY DIFFRACTION4( CHAIN C AND RESID 1:5 )C1 - 5
5X-RAY DIFFRACTION5( CHAIN C AND RESID 6:11 )C6 - 11
6X-RAY DIFFRACTION6( CHAIN C AND RESID 12:18 )C12 - 18
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:12 )D1 - 12
8X-RAY DIFFRACTION8( CHAIN D AND RESID 13:18 )D13 - 18
9X-RAY DIFFRACTION9( CHAIN A AND RESID 275:374 )A275 - 374
10X-RAY DIFFRACTION10( CHAIN A AND RESID 375:470 )A375 - 470
11X-RAY DIFFRACTION11( CHAIN A AND RESID 471:624 )A471 - 624
12X-RAY DIFFRACTION12( CHAIN E AND RESID 2:8 )E2 - 8
13X-RAY DIFFRACTION13( CHAIN E AND RESID 9:13 )E9 - 13
14X-RAY DIFFRACTION14( CHAIN E AND RESID 14:18 )E14 - 18
15X-RAY DIFFRACTION15( CHAIN G AND RESID 1:5 )G1 - 5
16X-RAY DIFFRACTION16( CHAIN G AND RESID 6:13 )G6 - 13
17X-RAY DIFFRACTION17( CHAIN G AND ( RESID 14:17 OR RESID 101:101 ) )G14 - 17
18X-RAY DIFFRACTION17( CHAIN G AND ( RESID 14:17 OR RESID 101:101 ) )G101

+
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