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- PDB-7xpk: crystal structure of rice ASI1 BAH domain in complex with a rice ... -

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Basic information

Entry
Database: PDB / ID: 7xpk
Titlecrystal structure of rice ASI1 BAH domain in complex with a rice SUVH6 peptide
Components
  • Alpha-aminoacylpeptide hydrolase
  • BAH domain-containing protein
KeywordsGENE REGULATION / BAH domain / ASI1 / rice / SUVH6 / H3K9me2 deposition
Function / homology
Function and homology information


histone methyltransferase activity / metallopeptidase activity / chromosome / nucleic acid binding / chromatin binding / endoplasmic reticulum / proteolysis / zinc ion binding / nucleus / membrane
Similarity search - Function
Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Bromo adjacent homology (BAH) domain / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Aminopeptidase N-type / ERAP1-like C-terminal domain ...Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Bromo adjacent homology (BAH) domain / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Post-SET domain / Post-SET domain profile. / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / PUA-like superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / Peptidase M4/M1, CTD superfamily / SET domain superfamily / SET domain profile. / SET domain / RNA-binding domain superfamily / SH3 type barrels. / Roll / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Beta
Similarity search - Domain/homology
Alpha-aminoacylpeptide hydrolase / BAH domain-containing protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYuan, J. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentJCYJ20200109110403829 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Molecular basis of locus-specific H3K9 methylation catalyzed by SUVH6 in plants.
Authors: Zhang, J. / Yuan, J. / Lin, J. / Chen, L. / You, L.Y. / Chen, S. / Peng, L. / Wang, C.H. / Du, J. / Duan, C.G.
History
DepositionMay 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BAH domain-containing protein
B: Alpha-aminoacylpeptide hydrolase
C: BAH domain-containing protein
D: Alpha-aminoacylpeptide hydrolase


Theoretical massNumber of molelcules
Total (without water)40,4234
Polymers40,4234
Non-polymers00
Water5,188288
1
A: BAH domain-containing protein
B: Alpha-aminoacylpeptide hydrolase


Theoretical massNumber of molelcules
Total (without water)20,2112
Polymers20,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-6 kcal/mol
Surface area10020 Å2
MethodPISA
2
C: BAH domain-containing protein
D: Alpha-aminoacylpeptide hydrolase


Theoretical massNumber of molelcules
Total (without water)20,2112
Polymers20,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-5 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.715, 72.939, 76.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BAH domain-containing protein


Mass: 18136.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: OsJ_02569 / Plasmid: pMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: B9EY07
#2: Protein/peptide Alpha-aminoacylpeptide hydrolase


Mass: 2074.500 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: A0A0E0IIA9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 30% PEG400 and 0.1 M CHES, pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2020
RadiationMonochromator: silicon crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 31676 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 19
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2996 / CC1/2: 0.712 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XPJ

7xpj


Resolution: 1.8→38.291 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1599 5.05 %
Rwork0.1996 --
obs0.2013 31676 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2831 0 0 288 3119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032892
X-RAY DIFFRACTIONf_angle_d0.6783888
X-RAY DIFFRACTIONf_dihedral_angle_d17.4641758
X-RAY DIFFRACTIONf_chiral_restr0.05413
X-RAY DIFFRACTIONf_plane_restr0.004500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8560.31561690.28342646X-RAY DIFFRACTION99
1.856-1.92240.34791450.26082702X-RAY DIFFRACTION100
1.9224-1.99930.29351370.24622690X-RAY DIFFRACTION100
1.9993-2.09030.26361220.24292730X-RAY DIFFRACTION100
2.0903-2.20050.27011720.23152678X-RAY DIFFRACTION100
2.2005-2.33840.26861700.21912686X-RAY DIFFRACTION100
2.3384-2.51890.26421250.22562727X-RAY DIFFRACTION100
2.5189-2.77230.23741460.22462750X-RAY DIFFRACTION100
2.7723-3.17330.23711590.20252737X-RAY DIFFRACTION100
3.1733-3.99730.21671380.17042792X-RAY DIFFRACTION100
3.9973-38.290.17081160.16482939X-RAY DIFFRACTION99

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