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- PDB-3vv0: Crystal structure of histone methyltransferase SET7/9 in complex ... -

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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


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 / heterochromatin organization / PKMTs methylate histone lysines / p53 binding ...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 / heterochromatin organization / PKMTs methylate histone lysines / p53 binding / chromatin organization / chromosome / response to ethanol / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / 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-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 ...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-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 superfamily / SET domain / 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

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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)29,5782
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

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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: 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

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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: 2.31 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

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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

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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: 2.001→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

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