[English] 日本語
Yorodumi
- PDB-5ciy: Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ciy
TitleStructural basis of the recognition of H3K36me3 by DNMT3B PWWP domain
Components
  • DNA (5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*AP*GP*(3DR)P*GP*CP*AP*TP*GP*G)-3')
  • Modification methylase HhaI
KeywordsTRANSFERASE/DNA / CG-SPECIFICITY / CPG SEQUENCE / C5-METHYLCYTOSINE / NUCLEOTIDE FLIPPING / S-ADENOSYL-L-HOMOCYSTEINE / COMPLEX (METHYLTRANSFERASE- DNA) / transferase-DNA complex
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / methylation / DNA binding
Similarity search - Function
DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / 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 / Vaccinia Virus protein VP39 ...DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / 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 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Type II methyltransferase M.HhaI
Similarity search - Component
Biological speciesHaemophilus parahaemolyticus (bacteria)
Haemophilus haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.594 Å
AuthorsRondelet, G. / DAL MASO, T. / Willems, L. / Wouters, J.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B.
Authors: Rondelet, G. / Dal Maso, T. / Willems, L. / Wouters, J.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_remark ...audit_author / database_PDB_remark / database_PDB_rev / database_PDB_rev_record / pdbx_seq_map_depositor_info
Item: _audit_author.name / _database_PDB_remark.text / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 10, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Modification methylase HhaI
C: DNA (5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3')
D: DNA (5'-D(P*GP*TP*CP*AP*GP*(3DR)P*GP*CP*AP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,41312
Polymers44,2603
Non-polymers1,1539
Water11,422634
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-92 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.335, 95.335, 314.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-793-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Modification methylase HhaI / M.HhaI / Cytosine-specific methyltransferase HhaI


Mass: 37042.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parahaemolyticus (bacteria)
Gene: hhaIM / Plasmid: pUHE25HhaI / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): ER1727
References: UniProt: P05102, DNA (cytosine-5-)-methyltransferase

-
DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3')


Mass: 3623.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus haemolyticus (bacteria)
#3: DNA chain DNA (5'-D(P*GP*TP*CP*AP*GP*(3DR)P*GP*CP*AP*TP*GP*G)-3')


Mass: 3594.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus haemolyticus (bacteria)

-
Non-polymers , 3 types, 643 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: AMMONIUM SULFATE 1.8 M, CITRATE 50mM

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2014 / Details: X-RAY FLUORESCCENCE DETECTOR
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL-CUT SI[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 72764 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 20.62 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Χ2: 0.969 / Net I/σ(I): 25.05 / Num. measured all: 477758
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.59-1.690.8370.6942.083581211812109550.80892.7
1.69-1.810.9440.366.565777011118110110.39999
1.81-1.950.9920.15215.367841310369103660.163100
1.95-2.140.9970.07824.3772215956095590.084100
2.14-2.390.9980.05333.5466380867486710.057100
2.39-2.760.9990.0439.6159044768476820.043100
2.76-3.370.9990.03247.7450035654565420.035100
3.37-4.760.9990.02953.937691513951140.03199.5
4.760.9990.02453.1320398297128640.02696.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.13 Å47.67 Å
Translation7.13 Å47.67 Å

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9MHT

9mht


Resolution: 1.594→36.554 Å / FOM work R set: 0.8394 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1883 3634 5 %
Rwork0.1653 69065 -
obs0.1664 72699 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.53 Å2 / Biso mean: 20.16 Å2 / Biso min: 9.47 Å2
Refinement stepCycle: final / Resolution: 1.594→36.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 484 66 634 3790
Biso mean--22.2 30.67 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063262
X-RAY DIFFRACTIONf_angle_d1.1614506
X-RAY DIFFRACTIONf_chiral_restr0.072482
X-RAY DIFFRACTIONf_plane_restr0.005495
X-RAY DIFFRACTIONf_dihedral_angle_d17.1211255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5941-1.6150.70861180.64952257237584
1.615-1.63720.49241290.51072466259593
1.6372-1.66050.43381320.41772501263395
1.6605-1.68530.3391360.34442581271797
1.6853-1.71170.3791380.30852623276198
1.7117-1.73970.33381400.29052659279999
1.7397-1.76970.27521400.23052656279699
1.7697-1.80190.26521390.186826382777100
1.8019-1.83660.19981410.156526802821100
1.8366-1.8740.17221410.160426872828100
1.874-1.91480.20221410.15126642805100
1.9148-1.95930.18681400.156226702810100
1.9593-2.00830.20761420.152826982840100
2.0083-2.06260.17931410.153326812822100
2.0626-2.12330.21551410.153126832824100
2.1233-2.19180.21461420.152726842826100
2.1918-2.27020.19311420.154627012843100
2.2702-2.3610.18941410.158126892830100
2.361-2.46850.18861430.160927052848100
2.4685-2.59860.18511410.162326912832100
2.5986-2.76130.19071440.16427172861100
2.7613-2.97450.19181430.163227252868100
2.9745-3.27360.16221430.154827192862100
3.2736-3.74690.13651440.132427372881100
3.7469-4.71910.12871450.12482753289899
4.7191-36.56410.15741470.16022800294797

+
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://pdbjlvh1.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