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- PDB-3m58: SET7/9 Y245A in complex with TAF10-K189me1 peptide and AdoHcy -

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Basic information

Entry
Database: PDB / ID: 3m58
TitleSET7/9 Y245A in complex with TAF10-K189me1 peptide and AdoHcy
Components
  • Histone-lysine N-methyltransferase SETD7
  • TAF10-K189me1 Peptide
KeywordsTRANSFERASE / TERNARY COMPLEX / SET DOMAIN / METHYLTRANSFERASE / S-ADENOSYL-L-HOMOCYSTEINE / TAF10 PEPTIDE / N-MONOMETHYLLYSINE / Chromatin regulator / Chromosomal protein / S-adenosyl-L-methionine / Transcription / Transcription regulation
Function / homology
Function and homology information


SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / transcription factor TFTC complex / hepatocyte differentiation ...SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / transcription factor TFTC complex / hepatocyte differentiation / protein-lysine N-methyltransferase activity / RNA polymerase binding / limb development / SAGA complex / transcription preinitiation complex / histone H3 methyltransferase activity / RNA polymerase II general transcription initiation factor activity / histone methyltransferase activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / regulation of RNA splicing / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / somitogenesis / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / nuclear estrogen receptor binding / male germ cell nucleus / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / G1/S transition of mitotic cell cycle / PKMTs methylate histone lysines / multicellular organism growth / p53 binding / chromosome / HATs acetylate histones / chromatin organization / response to ethanol / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / Ub-specific processing proteases / chromatin remodeling / apoptotic process / DNA damage response / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / enzyme binding / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
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 / Transcription initiation factor TFIID 23-30kDa subunit ...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 / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / Single Sheet / Beta Complex / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Transcription initiation factor TFIID subunit 10 / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsDel Rizzo, P.A. / Couture, J.-F. / Roiko, M.S. / Strunk, B.S. / Brunzelle, J.S. / Dirk, L.M. / Houtz, R.L. / Trievel, R.C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation.
Authors: Del Rizzo, P.A. / Couture, J.F. / Dirk, L.M. / Strunk, B.S. / Roiko, M.S. / Brunzelle, J.S. / Houtz, R.L. / Trievel, R.C.
History
DepositionMar 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD7
B: TAF10-K189me1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7965
Polymers30,2202
Non-polymers5773
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-26 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.210, 83.210, 95.264
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 28951.236 Da / Num. of mol.: 1 / Fragment: UNP residues 110-366 / Mutation: Y245A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: 9606 / Gene: KIAA1717, KMT7, SET7, SET9, SETD7 / Plasmid: pHIS2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Protein/peptide TAF10-K189me1 Peptide


Mass: 1268.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12962*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.9 M Ammonium Sulfate, 0.1 M Bis-Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0093 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 1.4→35 Å / Num. obs: 74675 / % possible obs: 98.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 22.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.4-1.455.60.432196.7
1.45-1.517.20.3391100
1.51-1.587.80.2261100
1.58-1.667.80.1591100
1.66-1.767.90.111100
1.76-1.980.0751100
1.9-2.097.90.061100
2.09-2.397.80.0481100
2.39-3.027.80.0371100
3.02-356.50.033190.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.66 Å33.7 Å
Translation1.66 Å33.7 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F69

2f69


Resolution: 1.4→33.71 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.485 / SU ML: 0.027 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19784 3745 5 %RANDOM
Rwork0.17498 ---
obs0.17613 70869 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.007 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 36 347 2418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222248
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.983086
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72624.158101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81415357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1371511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211749
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3851.51375
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.22322242
X-RAY DIFFRACTIONr_scbond_it3.963873
X-RAY DIFFRACTIONr_scangle_it4.3534.5827
X-RAY DIFFRACTIONr_rigid_bond_restr3.8432248
X-RAY DIFFRACTIONr_sphericity_free5.9523347
X-RAY DIFFRACTIONr_sphericity_bonded5.53932174
LS refinement shellResolution: 1.4→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 262 -
Rwork0.3 5028 -
obs--95.76 %

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