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- PDB-4ypa: ASH1L SET domain Q2265A mutant in complex with S-adenosyl methion... -

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Basic information

Entry
Database: PDB / ID: 4ypa
TitleASH1L SET domain Q2265A mutant in complex with S-adenosyl methionine (SAM)
ComponentsHistone-lysine N-methyltransferase ASH1L
KeywordsTRANSFERASE / histone methylation / SET domain
Function / homology
Function and homology information


uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / uterus morphogenesis / [histone H3]-lysine36 N-trimethyltransferase / [histone H3]-lysine9 N-methyltransferase / histone H3K36 trimethyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K36 methyltransferase activity ...uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / uterus morphogenesis / [histone H3]-lysine36 N-trimethyltransferase / [histone H3]-lysine9 N-methyltransferase / histone H3K36 trimethyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K36 methyltransferase activity / flagellated sperm motility / 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 / skeletal system development / post-embryonic 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 / zinc ion binding / nucleoplasm / nucleus
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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRogawski, D.S. / Ndoj, J. / Cho, H.J. / Maillard, I. / Grembecka, J. / Cierpicki, T.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01CA160467 United States
Leukemia & Lymphoma Society6111-14 United States
Leukemia & Lymphoma Society1215-14 United States
American Cancer SocietyRSG-13-130-01-CDD United States
Michigan Economic Development Corporation085P1000817 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008597 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM007863 United States
CitationJournal: Biochemistry / Year: 2015
Title: Two Loops Undergoing Concerted Dynamics Regulate the Activity of the ASH1L Histone Methyltransferase.
Authors: Rogawski, D.S. / Ndoj, J. / Cho, H.J. / Maillard, I. / Grembecka, J. / Cierpicki, T.
History
DepositionMar 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 4, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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_conn
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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase ASH1L
B: Histone-lysine N-methyltransferase ASH1L
C: Histone-lysine N-methyltransferase ASH1L
D: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,21720
Polymers103,8384
Non-polymers2,37916
Water3,855214
1
A: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5545
Polymers25,9591
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5545
Polymers25,9591
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5545
Polymers25,9591
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5545
Polymers25,9591
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.682, 61.773, 73.233
Angle α, β, γ (deg.)91.570, 93.830, 90.460
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2069 - 2280
2114C2069 - 2280
1124B2069 - 2280
2124D2069 - 2280

NCS ensembles :
ID
1
2

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Components

#1: Protein
Histone-lysine N-methyltransferase ASH1L / ASH1-like protein / huASH1 / Absent small and homeotic disks protein 1 homolog / Lysine N-methyltransferase 2H


Mass: 25959.465 Da / Num. of mol.: 4 / Fragment: SET domain (UNP residues 2074-2293) / Mutation: Q2265A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH1L, KIAA1420, KMT2H / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NR48, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Zn
#3: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, magnesium chloride, Tris / PH range: 8.3-8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 40091 / % possible obs: 96 % / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Χ2: 1.251 / Net I/av σ(I): 15.471 / Net I/σ(I): 8.1 / Num. measured all: 79637
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 % / Rejects: _

Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.340.25520230.79497.3
2.34-2.380.21820040.8197.5
2.38-2.430.1920820.78597.7
2.43-2.480.15520220.79997.2
2.48-2.530.14820370.80197.3
2.53-2.590.13620240.81897.3
2.59-2.660.12120190.8697.4
2.66-2.730.10620370.90597
2.73-2.810.10520450.94897.1
2.81-2.90.09619871.11197.1
2.9-30.08520441.16497.2
3-3.120.07320261.19396
3.12-3.260.06219761.21495.5
3.26-3.440.05720111.31395.8
3.44-3.650.05120101.41995.6
3.65-3.930.04719561.52594.6
3.93-4.330.04919581.91993.6
4.33-4.950.04419431.89593
4.95-6.240.04219792.70394.9
6.24-500.04319082.25291.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YNM

4ynm


Resolution: 2.3→73.04 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.868 / SU B: 9.634 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.528 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.303 2003 5 %RANDOM
Rwork0.2489 ---
obs0.2517 38087 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.29 Å2 / Biso mean: 38.039 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0.15 Å2-0.15 Å2
2--0.16 Å2-0.09 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 2.3→73.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6920 0 120 214 7254
Biso mean--26.12 36.19 -
Num. residues----858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0217188
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9579682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7885854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50624.105380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.956151264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5461556
X-RAY DIFFRACTIONr_chiral_restr0.1080.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215556
X-RAY DIFFRACTIONr_mcbond_it0.9871.54272
X-RAY DIFFRACTIONr_mcangle_it1.83626862
X-RAY DIFFRACTIONr_scbond_it2.53832916
X-RAY DIFFRACTIONr_scangle_it4.0414.52820
Refine LS restraints NCS

Dom-ID: 1 / Number: 1712 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.380.5
1AMEDIUM THERMAL1.062
2BMEDIUM POSITIONAL0.330.5
2BMEDIUM THERMAL0.862
LS refinement shellResolution: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 136 -
Rwork0.293 2758 -
all-2894 -
obs--93.17 %

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