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- PDB-3ope: Structural Basis of Auto-inhibitory mechanism of Histone methyltr... -

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Basic information

Entry
Database: PDB / ID: 3ope
TitleStructural Basis of Auto-inhibitory mechanism of Histone methyltransferase
ComponentsProbable histone-lysine N-methyltransferase ASH1L
KeywordsTRANSFERASE / SET / methyltransferase / nucleus
Function / homology
Function and homology information


uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / uterus morphogenesis / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / flagellated sperm motility ...uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / uterus morphogenesis / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / flagellated sperm motility / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / histone H3 methyltransferase activity / negative regulation of acute inflammatory response / decidualization / bicellular tight junction / single fertilization / negative regulation of MAPK cascade / post-embryonic development / skeletal system development / PKMTs methylate histone lysines / MAPK cascade / chromosome / methylation / transcription by RNA polymerase II / inflammatory response / chromatin binding / regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Beta-clip-like ...ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Beta-clip-like / SET domain / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Beta Complex / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase ASH1L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsAn, S. / Song, J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structure of the human histone methyltransferase ASH1L catalytic domain and its implications for the regulatory mechanism
Authors: An, S. / Yeo, K.J. / Jeon, Y.H. / Song, J.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Dec 11, 2019Group: Advisory / Database references / Derived calculations
Category: pdbx_validate_close_contact / struct_conn ...pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Mar 20, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_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

Downloads & links

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Assembly

Deposited unit
A: Probable histone-lysine N-methyltransferase ASH1L
B: Probable histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,56210
Polymers51,3722
Non-polymers1,1898
Water48627
1
A: Probable histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2815
Polymers25,6861
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2815
Polymers25,6861
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.530, 59.530, 233.804
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 Probable histone-lysine N-methyltransferase ASH1L / Absent small and homeotic disks protein 1 homolog / ASH1-like protein / huASH1 / Lysine N-methyltransferase 2H


Mass: 25686.111 Da / Num. of mol.: 2 / Fragment: SET domain (UNP RESIDUES 2074-2293)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH1L, KIAA1420, KMT2H / Plasmid: pET28a(modified) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NR48, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.33 Å3/Da / Density % sol: 47.16 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Bistrisprofane, PEG, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2827 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 19766 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 46.1
Reflection shellResolution: 2.9→2.95 Å / Mean I/σ(I) obs: 4.7 / Num. unique all: 541 / Rsym value: 0.62 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→50 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber / Details: The file contains Friedel pairs.
RfactorNum. reflectionSelection details
Rfree0.2994 963 RANDOM
Rwork0.2348 --
obs-18803 -
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 60 27 3391
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.73975
X-RAY DIFFRACTIONc_bond_d0.009299

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