[English] 日本語
Yorodumi
- PDB-6z2a: Structure of Clr4 mutant - F256A/F310A/F427A bound to SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z2a
TitleStructure of Clr4 mutant - F256A/F310A/F427A bound to SAH
Components(Histone-lysine N-methyltransferase, H3 lysine-9 ...) x 2
KeywordsTRANSFERASE / H3K9 methyltransferase / Heterochromatin
Function / homology
Function and homology information


CLRC complex / positive regulation of pericentric heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 monomethyltransferase activity / siRNA-mediated pericentric heterochromatin formation / [histone H3]-lysine9 N-methyltransferase ...CLRC complex / positive regulation of pericentric heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 monomethyltransferase activity / siRNA-mediated pericentric heterochromatin formation / [histone H3]-lysine9 N-methyltransferase / ubiquitin-modified histone reader activity / chromosome, subtelomeric region / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / pericentric heterochromatin formation / protein-lysine N-methyltransferase activity / spindle pole body / silent mating-type cassette heterochromatin formation / histone methyltransferase activity / pericentric heterochromatin / histone reader activity / ubiquitin binding / methyltransferase activity / single-stranded DNA binding / methylation / double-stranded DNA binding / single-stranded RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Histone H3-K9 methyltransferase / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Histone H3-K9 methyltransferase / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase, H3 lysine-9 specific
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.456 Å
AuthorsStirpe, A. / Schalch, T.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_139137 Switzerland
Swiss National Science FoundationPP00P3_163760_1 Switzerland
Swiss National Science FoundationPP00P3_172904 Switzerland
CitationJournal: Elife / Year: 2021
Title: SUV39 SET domains mediate crosstalk of heterochromatic histone marks.
Authors: Stirpe, A. / Guidotti, N. / Northall, S.J. / Kilic, S. / Hainard, A. / Vadas, O. / Fierz, B. / Schalch, T.
History
DepositionMay 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,90114
Polymers66,5602
Non-polymers1,34112
Water39622
1
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0377
Polymers33,3661
Non-polymers6706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8647
Polymers33,1941
Non-polymers6706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.444, 110.288, 70.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 196 - 489

Dom-IDAuth asym-IDLabel asym-IDLabel seq-ID
1AA2 - 295
2BB1 - 294

-
Components

-
Histone-lysine N-methyltransferase, H3 lysine-9 ... , 2 types, 2 molecules AB

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific / Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / HKMT / Lysine N-methyltransferase 1 / ...Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / HKMT / Lysine N-methyltransferase 1 / Protein lysine methyltransferase clr4 / PKMT


Mass: 33366.195 Da / Num. of mol.: 1 / Mutation: F256A, F310A, F427A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: clr4, kmt1, SPBC428.08c / Cell line (production host): RosettaII / Production host: Escherichia coli (E. coli)
References: UniProt: O60016, [histone H3]-lysine9 N-trimethyltransferase
#2: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific / Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / HKMT / Lysine N-methyltransferase 1 / ...Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / HKMT / Lysine N-methyltransferase 1 / Protein lysine methyltransferase clr4 / PKMT


Mass: 33194.059 Da / Num. of mol.: 1 / Mutation: F256A, F310A, F427A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: clr4, kmt1, SPBC428.08c / Cell line (production host): RosettaII / Production host: Escherichia coli (E. coli)
References: UniProt: O60016, [histone H3]-lysine9 N-trimethyltransferase

-
Non-polymers , 4 types, 34 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 71.4 mM MES, 28.6 mM Imidazole, 20% PEG 10000, 30mM Magnesium Acetate, 6.6% v/v MPD, 6.6% v/v PEG 1000, 6.6% v/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2018
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.456→70.68 Å / Num. obs: 19571 / % possible obs: 72.2 % / Redundancy: 6.1 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.093 / Rrim(I) all: 0.233 / Net I/σ(I): 6.6
Reflection shellResolution: 2.456→2.68 Å / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 979 / CC1/2: 0.627 / CC star: 0.878 / Rpim(I) all: 0.525 / Rrim(I) all: 1.046

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BOX

6box


Resolution: 2.456→70.68 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.91 / SU B: 24.391 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 1.848 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 973 5 %RANDOM
Rwork0.23851 ---
obs0.23909 18561 72.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.086 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.54 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.456→70.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4411 0 62 22 4495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134595
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174005
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.6766258
X-RAY DIFFRACTIONr_angle_other_deg1.2271.5829313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61321.898274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.70415727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3631538
X-RAY DIFFRACTIONr_chiral_restr0.0560.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021026
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7321.8762237
X-RAY DIFFRACTIONr_mcbond_other0.7321.8762237
X-RAY DIFFRACTIONr_mcangle_it1.3732.8022784
X-RAY DIFFRACTIONr_mcangle_other1.3732.8022785
X-RAY DIFFRACTIONr_scbond_it0.491.9142358
X-RAY DIFFRACTIONr_scbond_other0.491.9142358
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8542.8533475
X-RAY DIFFRACTIONr_long_range_B_refined3.96332.15814617
X-RAY DIFFRACTIONr_long_range_B_other3.96232.15614614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8152 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.456→2.52 Å
RfactorNum. reflection% reflection
Rfree0.736 1 -
Rwork0.396 41 -
obs--2.1 %
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)
10.65060.91970.06044.47780.63152.4630.0317-0.06840.12040.19670.17630.0278-0.30170.2551-0.2080.1474-0.01690.01210.0524-0.03930.0534-21.989-5.5746-1.7889
20.9339-0.733-0.83653.44140.38674.6575-0.1696-0.0409-0.186-0.06260.1565-0.24730.56760.29210.01310.16030.03480.02290.0265-0.02410.1047-19.3178-35.2017-15.2761
30.95840.1001-0.79553.21680.21543.5353-0.01660.0556-0.0338-0.02640.0890.2305-0.0317-0.19-0.07250.03880.0029-0.02870.01360.00890.0463-30.6729-17.1929-11.5964
42.5824-1.9444-1.3882.17860.36157.2625-0.068-0.0866-0.10860.04430.08810.2312-0.1107-0.3366-0.02010.07470.0146-0.02730.13620.03560.1816-42.532-7.3138-19.1401
51.2379-0.9161-0.16053.65220.54242.69540.11120.0615-0.1074-0.18290.1709-0.00880.3450.3011-0.28210.12260.0208-0.02820.0537-0.04780.0491-21.803715.529-33.4415
61.41590.45530.6762.9780.48674.005-0.1714-0.00020.23390.04550.1614-0.1867-0.630.27150.00990.163-0.0445-0.01840.0327-0.03250.1007-19.404545.0687-20.0797
70.9724-0.13380.58632.87390.03783.3419-0.0085-0.04450.02680.06530.03110.18310.0483-0.1241-0.02260.0216-0.00110.02690.00550.00150.0429-30.17127.0346-23.6435
83.2925-1.9334-0.10434.19661.13598.24140.26520.06070.1739-0.138-0.160.5001-0.1195-0.5938-0.10520.0788-0.04540.03970.15840.050.2308-42.829519.1517-17.2015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A192 - 248
2X-RAY DIFFRACTION2A249 - 329
3X-RAY DIFFRACTION3A330 - 462
4X-RAY DIFFRACTION4A463 - 490
5X-RAY DIFFRACTION5B192 - 248
6X-RAY DIFFRACTION6B249 - 329
7X-RAY DIFFRACTION7B330 - 462
8X-RAY DIFFRACTION8B463 - 490

+
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