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- PDB-3s8s: Crystal structure of the RRM domain of human SETD1A -

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Basic information

Entry
Database: PDB / ID: 3s8s
TitleCrystal structure of the RRM domain of human SETD1A
ComponentsHistone-lysine N-methyltransferase SETD1A
KeywordsTRANSCRIPTION / chromatin modification / transcription regulation / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of chromatin organization / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / histone H3K4 methyltransferase activity / regulation of hematopoietic stem cell differentiation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / brain development ...regulation of chromatin organization / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / histone H3K4 methyltransferase activity / regulation of hematopoietic stem cell differentiation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / brain development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / beta-catenin binding / methylation / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear speck / DNA damage response / chromatin / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Set1A, RNA recognition motif / Histone-lysine N-methyltransferase SETD1A / Histone-lysine N-methyltransferase Set1-like / COMPASS complex Set1 subunit, N-SET domain / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain ...Set1A, RNA recognition motif / Histone-lysine N-methyltransferase SETD1A / Histone-lysine N-methyltransferase Set1-like / COMPASS complex Set1 subunit, N-SET domain / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase SETD1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsChao, X. / Tempel, W. / Bian, C. / Cerovina, T. / Walker, J.R. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the RRM domain of human SETD1A
Authors: Chao, X. / Tempel, W. / Bian, C. / Cerovina, T. / Walker, J.R. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionMay 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD1A


Theoretical massNumber of molelcules
Total (without water)12,48618
Polymers12,4861
Non-polymers017
Water1,72996
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.650, 31.510, 39.320
Angle α, β, γ (deg.)90.000, 114.120, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Histone-lysine N-methyltransferase SETD1A / Lysine N-methyltransferase 2F / SET domain-containing protein 1A / hSET1A / Set1/Ash2 histone ...Lysine N-methyltransferase 2F / SET domain-containing protein 1A / hSET1A / Set1/Ash2 histone methyltransferase complex subunit SET1


Mass: 12486.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD1A, KIAA0339, KMT2F, SET1, SET1A / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O15047
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.61 Å3/Da / Density % sol: 23.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 1.5 M ammonium sulfate, 0.1 M bistris propane, pH 7.0, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97941 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 1.3→31.29 Å / Num. obs: 19651 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.625 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.3-1.330.7051.94712141096.3
1.33-1.370.6072.35069143599.6
1.37-1.410.4672.94882137499.4
1.41-1.450.3943.64739131899.5
1.45-1.50.3034.74690130099.3
1.5-1.550.2425.54426123199.6
1.55-1.610.1946.74482123399.8
1.61-1.680.1648.14209114799.7
1.68-1.750.1299.64130112999.4
1.75-1.840.09312.63966107599.3
1.84-1.940.07515.73646101599.7
1.94-2.060.05619.2353096498.8
2.06-2.20.0522.1324889998
2.2-2.370.04524.6301883698.2
2.37-2.60.04226.7286378198.6
2.6-2.910.03928.3255570598.9
2.91-3.360.03430.5221761498.2
3.36-4.110.03233.2189152896.9
4.11-5.810.03134.2150141998.4
5.810.0332.579723896

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: composite of pdb entries 3LPY and 2J8A

3lpy

2j8a


Resolution: 1.3→31.29 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.95 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs BUCCANEER and COOT were also used during refinement. The MOLPROBITY server was used for model geometry validation. Significant ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs BUCCANEER and COOT were also used during refinement. The MOLPROBITY server was used for model geometry validation. Significant difference density remains for the current model around the side chain of residue His-166.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 995 5.1 %RANDOM
Rwork0.168 ---
obs0.17 19618 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.2 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.3→31.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 17 96 963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022916
X-RAY DIFFRACTIONr_bond_other_d0.0010.02631
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9661252
X-RAY DIFFRACTIONr_angle_other_deg0.89131554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6575123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81523.33339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.51915177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.439157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02180
X-RAY DIFFRACTIONr_mcbond_it1.1581.5558
X-RAY DIFFRACTIONr_mcbond_other0.3791.5225
X-RAY DIFFRACTIONr_mcangle_it1.9662923
X-RAY DIFFRACTIONr_scbond_it2.7523358
X-RAY DIFFRACTIONr_scangle_it4.3424.5320
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 62 -
Rwork0.257 1345 -
all-1407 -
obs--96.37 %

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