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- PDB-7yf3: Crystal structure of METTL9 in complex with unmethylated S100A9 p... -

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Basic information

Entry
Database: PDB / ID: 7yf3
TitleCrystal structure of METTL9 in complex with unmethylated S100A9 peptide and SAH
Components
  • Protein-L-histidine N-pros-methyltransferase
  • S100A9 peptide
KeywordsTRANSFERASE / METTL9 / S100A9 / histidine methyltransferase
Function / homology
Function and homology information


protein-L-histidine N-pros-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / endoplasmic reticulum / mitochondrion
Similarity search - Function
Protein-L-histidine N-pros-methyltransferase / DREV methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Protein-L-histidine N-pros-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.434 Å
AuthorsXie, H. / Wang, X. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2023
Title: Molecular basis for METTL9-mediated N1-histidine methylation.
Authors: Wang, X. / Xie, H. / Guo, Q. / Cao, D. / Ru, W. / Zhao, S. / Zhu, Z. / Zhang, J. / Pan, W. / Yao, X. / Xu, C.
History
DepositionJul 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / entity_src_gen / pdbx_entity_src_syn
Item: _entity.src_method
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-L-histidine N-pros-methyltransferase
B: Protein-L-histidine N-pros-methyltransferase
C: S100A9 peptide
D: S100A9 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1196
Polymers65,3504
Non-polymers7692
Water00
1
A: Protein-L-histidine N-pros-methyltransferase
C: S100A9 peptide
hetero molecules

B: Protein-L-histidine N-pros-methyltransferase
D: S100A9 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1196
Polymers65,3504
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area3390 Å2
ΔGint-23 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.892, 43.547, 106.492
Angle α, β, γ (deg.)90.000, 123.700, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein-L-histidine N-pros-methyltransferase / DORA reverse strand protein / DREV / DREV1 / Methyltransferase-like protein 9 / hMETTL9 / METTL9


Mass: 31554.012 Da / Num. of mol.: 2 / Mutation: L95A, F96A, L99A, F103A, V107A, F111A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL9, DREV, CGI-81 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H1A3, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein/peptide S100A9 peptide


Mass: 1121.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 0.2 M MgCl2, 30% (w/v) PEG 4000, 0.1 M NDSB-256

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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 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.43→70.32 Å / Num. obs: 7067 / % possible obs: 94.7 % / Redundancy: 6.3 % / CC1/2: 0.984 / Net I/σ(I): 5.8
Reflection shellResolution: 3.43→3.64 Å / Num. unique obs: 7067 / CC1/2: 0.797

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YF2

7yf2


Resolution: 3.434→70.319 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2881 708 10.02 %
Rwork0.2356 6359 -
obs0.2407 7067 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.48 Å2 / Biso mean: 60.1084 Å2 / Biso min: 47.27 Å2
Refinement stepCycle: final / Resolution: 3.434→70.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4275 0 52 0 4327
Biso mean--56.25 --
Num. residues----543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.434-3.69890.36381190.307107381
3.6989-4.07110.331440.2479129997
4.0711-4.66010.28181470.2179131498
4.6601-5.87080.28381460.2404131998
5.8708-70.3190.24481520.2143135496

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