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- PDB-8ilz: Crystal structure of the RRM domain of human SETD1B -

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Basic information

Entry
Database: PDB / ID: 8ilz
TitleCrystal structure of the RRM domain of human SETD1B
ComponentsHistone-lysine N-methyltransferase SETD1B
KeywordsSTRUCTURAL PROTEIN / SETD1B / RRM domain
Function / homology
Function and homology information


[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / histone H3 methyltransferase activity / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / chromosome ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / histone H3 methyltransferase activity / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / chromosome / methylation / nuclear speck / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Set1B, 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 ...Set1B, 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 / 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
Similarity search - Domain/homology
Histone-lysine N-methyltransferase SETD1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Molecular insight into the SETD1A/B N-terminal region and its interaction with WDR82.
Authors: Bao, S. / Xu, C.
History
DepositionMar 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD1B


Theoretical massNumber of molelcules
Total (without water)11,8371
Polymers11,8371
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.575, 70.575, 37.573
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Histone-lysine N-methyltransferase SETD1B / Lysine N-methyltransferase 2G / SET domain-containing protein 1B / hSET1B


Mass: 11836.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD1B, KIAA1076, KMT2G, SET1B / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UPS6, [histone H3]-lysine4 N-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium acetate trihydrate, 0.1 M TRIS hydrochloride pH 9.0, 27% PEG 4000, 9% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.77→35.29 Å / Num. obs: 10501 / % possible obs: 99.46 % / Redundancy: 18.8 % / Biso Wilson estimate: 21.22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05294 / Net I/σ(I): 35.29
Reflection shellResolution: 1.77→1.81 Å / Rmerge(I) obs: 0.4609 / Num. unique obs: 10501 / CC1/2: 0.813

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT1.20.1_4487data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→35.29 Å / SU ML: 0.1697 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1679
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 478 4.55 %
Rwork0.1768 10023 -
obs0.1786 10501 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.72 Å2
Refinement stepCycle: LAST / Resolution: 1.77→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 0 104 930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006841
X-RAY DIFFRACTIONf_angle_d0.86941133
X-RAY DIFFRACTIONf_chiral_restr0.0641131
X-RAY DIFFRACTIONf_plane_restr0.0064142
X-RAY DIFFRACTIONf_dihedral_angle_d5.327112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-2.030.25971590.19773276X-RAY DIFFRACTION98.57
2.03-2.550.22821540.19093342X-RAY DIFFRACTION99.94
2.55-35.290.19921650.16643405X-RAY DIFFRACTION99.92

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