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- PDB-3ru0: Cocrystal structure of human SMYD3 with inhibitor Sinefungin bound -

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Basic information

Entry
Database: PDB / ID: 3ru0
TitleCocrystal structure of human SMYD3 with inhibitor Sinefungin bound
ComponentsSET and MYND domain-containing protein 3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / methyltransferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines ...histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines / nucleosome assembly / positive regulation of peptidyl-serine phosphorylation / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. ...Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Annexin V; domain 1 / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / Helix Hairpins / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
SINEFUNGIN / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.849 Å
AuthorsForeman, K.W. / Brown, M. / Park, F. / Emtage, S. / Harriss, J. / Das, C. / Zhu, L. / Crew, A. / Arnold, L. / Shaaban, S. / Tucker, P.
CitationJournal: Plos One / Year: 2011
Title: Structural and Functional Profiling of the Human Histone Methyltransferase SMYD3.
Authors: Foreman, K.W. / Brown, M. / Park, F. / Emtage, S. / Harriss, J. / Das, C. / Zhu, L. / Crew, A. / Arnold, L. / Shaaban, S. / Tucker, P.
History
DepositionMay 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Feb 28, 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 / 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 / _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.ptnr2_auth_asym_id / _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.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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: SET and MYND domain-containing protein 3
B: SET and MYND domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,85410
Polymers100,6992
Non-polymers1,1558
Water8,683482
1
A: SET and MYND domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9275
Polymers50,3491
Non-polymers5784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SET and MYND domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9275
Polymers50,3491
Non-polymers5784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.175, 118.073, 82.901
Angle α, β, γ (deg.)90.00, 91.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SET and MYND domain-containing protein 3 / Zinc finger MYND domain-containing protein 1


Mass: 50349.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9H7B4, histone-lysine N-methyltransferase
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.75ul of protein 10mg/mL and 1mM Sinefungin in 25mM TrisHCl pH7.6, 150mM NaCl, 1mM TCEP and 0.75uL reservoir solution: 100mM HEPES pH 7.5, 16% PEG 3350, 200mM Magnesium Chloride , VAPOR ...Details: 0.75ul of protein 10mg/mL and 1mM Sinefungin in 25mM TrisHCl pH7.6, 150mM NaCl, 1mM TCEP and 0.75uL reservoir solution: 100mM HEPES pH 7.5, 16% PEG 3350, 200mM Magnesium Chloride , VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.28146, 1.24294
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 22, 2005
RadiationMonochromator: DIAMOND / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.281461
21.242941
ReflectionResolution: 1.849→21.832 Å / Num. all: 94957 / Num. obs: 94957 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 18.4

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.849→21.832 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.216 -
Rwork0.2 -
all-94957
obs-94957
Refinement stepCycle: LAST / Resolution: 1.849→21.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 0 60 482 7063

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