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- PDB-1h3i: Crystal structure of the Histone Methyltransferase SET7/9 -

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Basic information

Entry
Database: PDB / ID: 1h3i
TitleCrystal structure of the Histone Methyltransferase SET7/9
ComponentsHISTONE H3 LYSINE 4 SPECIFIC METHYLTRANSFERASE
KeywordsTRANSFERASE / METHYLTRANSFERASE
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 / PKMTs methylate histone lysines / p53 binding ...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 / 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 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
Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsWilson, J.R. / Jing, C. / Walker, P.A. / Martin, S.R. / Howell, S.A. / Blackburn, G.M. / Gamblin, S.J. / Xiao, B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Crystal Structure and Functional Analysis of the Histone Methyltransferase Set7/9
Authors: Wilson, J.R. / Jing, C. / Walker, P.A. / Martin, S.R. / Howell, S.A. / Blackburn, G.M. / Gamblin, S.J. / Xiao, B.
History
DepositionSep 4, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTONE H3 LYSINE 4 SPECIFIC METHYLTRANSFERASE
B: HISTONE H3 LYSINE 4 SPECIFIC METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2175
Polymers65,1442
Non-polymers733
Water6,197344
1
A: HISTONE H3 LYSINE 4 SPECIFIC METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6213
Polymers32,5721
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HISTONE H3 LYSINE 4 SPECIFIC METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5962
Polymers32,5721
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.090, 82.830, 116.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HISTONE H3 LYSINE 4 SPECIFIC METHYLTRANSFERASE / HISTONE H3-K4 / METHYLTRANSFERASE


Mass: 32571.914 Da / Num. of mol.: 2 / Fragment: N-DOMAIN, SET-DOMAIN, RESIDUES 52-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris1droppH7.0
3100 mM1dropNaCl
41 mMTCEP1drop
50.2 Mmagnesium formate1reservoir
625 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794, 0.9394, 0.9800
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.93941
30.981
ReflectionResolution: 2.1→20 Å / Num. obs: 37053 / % possible obs: 95.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.067
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 84 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.048

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.105 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1820 5 %RANDOM
Rwork0.21 ---
obs0.212 34521 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2---2.43 Å20 Å2
3---3.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 3 344 4935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214708
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.956396
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7683584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79415781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023728
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2680.32228
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.5681
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.57
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.3103
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7232898
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.04654662
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.95261810
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.74981734
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 122
Rwork0.228 2404
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)
11.46060.68050.3931.0678-0.05693.9867-0.03660.18030.10980.02880.04980.09430.0080.0616-0.01320.23520.00320.04110.5732-0.00790.08815.12713.514-4.085
20.99840.68680.95951.65061.47343.95890.0367-0.1079-0.04760.1568-0.12610.16350.1854-0.17180.08940.208-0.00580.0260.5659-0.04510.1117-8.9984.038-19.414
31.6676-0.3177-0.9310.78940.39492.8105-0.0490.04120.05690.00410.0116-0.0032-0.0742-0.05930.03740.2357-0.0217-0.05580.5136-0.02840.1068-2.3650.314-43.873
41.1051-0.1205-0.56521.2182-0.05082.89470.0135-0.0280.06340.0056-0.0595-0.0339-0.25310.2380.0460.2546-0.0113-0.04830.5297-0.03580.10341.2763.743-44.368
59.7671-4.8112-1.212211.2864-2.30587.8401-0.3878-0.7989-0.71590.57740.27690.95070.2258-0.07970.11090.3410.07670.09110.55150.02420.0244-20.51823.69549.846
62.482-0.2542-2.23171.75010.38164.9226-0.222-0.4239-0.18730.3580.0167-0.0867-0.04270.35790.20530.28230.0519-0.02330.55120.03850.0127-3.87118.56234.434
70.5299-0.0841-0.20431.0621-0.45171.4887-0.0337-0.00730.04780.0442-0.0479-0.0776-0.14240.01260.08160.27650.0046-0.00650.5601-0.01830.1197-4.84527.21710.243
81.0341-0.0064-0.10961.4084-0.37821.9054-0.0189-0.04660.0674-0.0416-0.00730.057-0.2415-0.11230.02620.28640.0062-0.00130.5287-0.02040.1135-9.75328.0989.751
90.0801-0.1089-0.06540.22130.19340.5581-0.0172-0.0029-0.02720.0663-0.00430.02310.0886-0.04210.02150.226-0.0195-0.00230.51330.0040.0436-4.38813.597-6.573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 95
2X-RAY DIFFRACTION2A96 - 192
3X-RAY DIFFRACTION3A193 - 264
4X-RAY DIFFRACTION4A265 - 344
5X-RAY DIFFRACTION5B52 - 95
6X-RAY DIFFRACTION6B96 - 192
7X-RAY DIFFRACTION7B193 - 264
8X-RAY DIFFRACTION8B265 - 344
9X-RAY DIFFRACTION9W1 - 403
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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