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- PDB-3vuz: Crystal structure of histone methyltransferase SET7/9 in complex ... -

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Basic information

Entry
Database: PDB / ID: 3vuz
TitleCrystal structure of histone methyltransferase SET7/9 in complex with AAM-1
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-K15 / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,5352
Polymers29,0831
Non-polymers4521
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.807, 39.223, 67.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: UNP 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-K15 / 5'-{[(3S)-3-amino-3-carboxypropyl](hexyl)amino}-5'-deoxyadenosine


Mass: 451.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H33N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.55 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9883 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 49.04 Å2 / Rsym value: 0.135 / Net I/σ(I): 16
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.625 / % possible all: 100

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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: 2.5→28.19 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.43 / σ(F): 1.34 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 560 5.73 %
Rwork0.1829 --
obs0.1864 9781 99.89 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.124 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 129.79 Å2 / Biso mean: 55.9884 Å2 / Biso min: 23.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.2514 Å2-0 Å20 Å2
2---8.2579 Å20 Å2
3---6.0066 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 32 69 2017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072005
X-RAY DIFFRACTIONf_angle_d1.1112725
X-RAY DIFFRACTIONf_dihedral_angle_d16.554724
X-RAY DIFFRACTIONf_chiral_restr0.07290
X-RAY DIFFRACTIONf_plane_restr0.004354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.75140.36581450.27112224
2.7514-3.14910.29121370.21552266
3.1491-3.96580.24961360.17812310
3.9658-28.19150.20651420.1592421
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)
13.69570.0795-0.73980.2364-0.23760.3430.0984-0.4210.67950.16330.0794-0.5422-0.12490.167-0.15340.31770.04370.02580.3986-0.07510.6642-1.22257.3409-13.0894
22.0946-0.9721-0.0133.7415-0.24062.17040.243-0.07020.126-0.5384-0.17980.4180.1828-0.2746-0.03430.2332-0.0188-0.01510.1610.01480.1133-26.65923.4259-18.3267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:162)A1 - 162
2X-RAY DIFFRACTION2chain 'A' and (resseq 163:362)A163 - 362

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