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- PDB-7y9c: Crystal structure of METTL9 in complex with SLC39A5 peptide and SAH -

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Basic information

Entry
Database: PDB / ID: 7y9c
TitleCrystal structure of METTL9 in complex with SLC39A5 peptide and SAH
Components
  • Protein-L-histidine N-pros-methyltransferase
  • SLC39A5
KeywordsTRANSFERASE / METTL9 / SLC39A5 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 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

Downloads & links

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Assembly

Deposited unit
A: Protein-L-histidine N-pros-methyltransferase
B: Protein-L-histidine N-pros-methyltransferase
C: SLC39A5
D: SLC39A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6286
Polymers65,8594
Non-polymers7692
Water7,098394
1
A: Protein-L-histidine N-pros-methyltransferase
C: SLC39A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3143
Polymers32,9292
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-10 kcal/mol
Surface area12950 Å2
MethodPISA
2
B: Protein-L-histidine N-pros-methyltransferase
D: SLC39A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3143
Polymers32,9292
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-9 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.280, 46.046, 124.780
Angle α, β, γ (deg.)90.000, 103.350, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-684-

HOH

21B-685-

HOH

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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 SLC39A5


Mass: 1375.390 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES monohydrate pH6.5, 12 % w/v PEG 20000, 0.2 M sodium thiocyanate

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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 PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→43.05 Å / Num. obs: 34530 / % possible obs: 99.6 % / Redundancy: 6.4 % / CC1/2: 0.998 / Net I/σ(I): 14.6
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 34530 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model from alphafold2

Resolution: 2.1→31.829 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 1699 4.92 %
Rwork0.192 32831 -
obs0.1945 34530 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.12 Å2 / Biso mean: 28.5783 Å2 / Biso min: 14.35 Å2
Refinement stepCycle: final / Resolution: 2.1→31.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4485 0 52 394 4931
Biso mean--22.06 30.72 -
Num. residues----563
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.16180.32221390.2399258495
2.1618-2.23160.30661640.2408268599
2.2316-2.31130.31651420.2709271399
2.3113-2.40380.24221400.20272710100
2.4038-2.51320.2611380.21052750100
2.5132-2.64560.24531490.19792697100
2.6456-2.81130.25361360.19572767100
2.8113-3.02820.26591520.20472736100
3.0282-3.33270.25131280.1922766100
3.3327-3.81420.20441160.16962790100
3.8142-4.80290.21131400.15822780100
4.8029-31.8290.21591550.18542853100

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