[English] 日本語
Yorodumi
- PDB-3vv0: Crystal structure of histone methyltransferase SET7/9 in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vv0
TitleCrystal structure of histone methyltransferase SET7/9 in complex with DAAM-3
ComponentsHistone-lysine N-methyltransferase SETD7
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SET domain / transferase / adenosylmethionine binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / regulation of DNA repair / PKMTs methylate histone lysines ...heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / regulation of DNA repair / PKMTs methylate histone lysines / p53 binding / chromosome / chromatin organization / response to ethanol / DNA damage response / chromatin binding / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / nucleus
Similarity search - Function
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / : / Histone H3 K4-specific methyltransferase SET7 N-terminal / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like ...Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / : / Histone H3 K4-specific methyltransferase SET7 N-terminal / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Single Sheet / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-KH3 / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsNiwa, H. / Handa, N. / Tomabechi, Y. / Honda, K. / Toyama, M. / Ohsawa, N. / Shirouzu, M. / Kagechika, H. / Hirano, T. / Umehara, T. / Yokoyama, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives
Authors: Niwa, H. / Handa, N. / Tomabechi, Y. / Honda, K. / Toyama, M. / Ohsawa, N. / Shirouzu, M. / Kagechika, H. / Hirano, T. / Umehara, T. / Yokoyama, S.
History
DepositionJul 10, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Sep 28, 2016Group: Structure summary
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5782
Polymers29,0831
Non-polymers4951
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.836, 39.126, 67.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Histone-lysine N-methyltransferase SETD7 / Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / Lysine N-methyltransferase 7 / SET ...Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / Lysine N-methyltransferase 7 / SET domain-containing protein 7 / SET7/9


Mass: 29083.244 Da / Num. of mol.: 1 / Fragment: residues 111-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Plasmid: PX100709-08 / Production host: CELL-FREE SYNTHESIS (others)
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Chemical ChemComp-KH3 / 5'-{[(3S)-3-amino-3-carboxypropyl][2-(hexylamino)ethyl]amino}-5'-deoxyadenosine


Mass: 494.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H38N8O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-HCl pH8.3-8.5, 28-30% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
PH range: 8.3-8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 24, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18855 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 33.37 Å2 / Rsym value: 0.081 / Net I/σ(I): 25.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.718 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1n6a

1n6a


Resolution: 2.001→28.176 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 1.33 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 1120 5.96 %
Rwork0.1863 --
obs0.1888 18802 99.86 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.86 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 119.32 Å2 / Biso mean: 47.0282 Å2 / Biso min: 17.77 Å2
Baniso -1Baniso -2Baniso -3
1-6.6979 Å2-0 Å2-0 Å2
2---5.9808 Å2-0 Å2
3----0.7171 Å2
Refinement stepCycle: LAST / Resolution: 2.001→28.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 35 119 2002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081934
X-RAY DIFFRACTIONf_angle_d1.0842628
X-RAY DIFFRACTIONf_dihedral_angle_d14.435702
X-RAY DIFFRACTIONf_chiral_restr0.073281
X-RAY DIFFRACTIONf_plane_restr0.004338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0012-2.09220.29171550.2357212699
2.0922-2.20250.26451420.21212153100
2.2025-2.34040.24881350.20022184100
2.3404-2.5210.26991360.19072193100
2.521-2.77450.2331520.19732187100
2.7745-3.17560.26951280.19672206100
3.1756-3.9990.21691340.16992258100
3.999-28.17930.19971380.17732375100
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)
15.57090.16370.11493.77910.93112.24030.2335-0.43990.50210.37970.1292-0.85660.03630.6008-0.17580.1956-0.0325-0.00140.3288-0.05720.4201-4.70597.0455-13.1603
22.5908-0.8420.25143.45380.14091.83290.1759-0.15840.6001-0.3152-0.3065-0.0813-0.0548-0.004-0.0240.20450.01020.07660.1131-0.00180.144-18.461610.1522-20.9854
31.3671-0.30040.02511.4513-1.32741.9884-0.0943-0.3386-0.24840.3779-0.12240.79650.4983-0.788-0.06650.381-0.18290.24130.5645-0.09550.3648-33.23850.5667-8.8511
42.8211-0.25120.25214.1955-0.54232.9850.1877-0.454-0.03290.2429-0.21180.84030.2266-0.36480.02690.2425-0.0550.05810.3153-0.04120.2749-28.63022.0572-15.8179
53.4599-0.3936-0.65363.98570.31463.1895-0.1123-0.0134-0.3302-0.8898-0.39271.67090.2563-0.9134-0.1710.4806-0.0716-0.14880.4134-0.14690.6559-36.1576-7.1519-26.0566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 116:162)A116 - 162
2X-RAY DIFFRACTION2chain 'A' and (resseq 163:240)A163 - 240
3X-RAY DIFFRACTION3chain 'A' and (resseq 241:262)A241 - 262
4X-RAY DIFFRACTION4chain 'A' and (resseq 263:321)A263 - 321
5X-RAY DIFFRACTION5chain 'A' and (resseq 322:362)A322 - 362

+
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