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- PDB-7yf4: Crystal structure of METTL9 in complex with SLC39A5 mutant peptid... -

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Basic information

Entry
Database: PDB / ID: 7yf4
TitleCrystal structure of METTL9 in complex with SLC39A5 mutant peptide and SAH
Components
  • Protein-L-histidine N-pros-methyltransferase
  • SLC39A5 mutant peptide
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 1.1Nov 29, 2023Group: 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 mutant peptide
D: SLC39A5 mutant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2436
Polymers65,4744
Non-polymers7692
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-19 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.387, 43.213, 106.231
Angle α, β, γ (deg.)90.000, 122.770, 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 SLC39A5 mutant peptide


Mass: 1183.197 Da / Num. of mol.: 2 / Mutation: S374A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL9, DREV, CGI-81 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.39 %
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 PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.75→59.86 Å / Num. obs: 14118 / % possible obs: 97.3 % / Redundancy: 5.9 % / CC1/2: 0.997 / Net I/σ(I): 9.9
Reflection shellResolution: 2.75→2.9 Å / Num. unique obs: 14118 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YF2

7yf2


Resolution: 2.75→59.86 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 1412 10 %
Rwork0.2228 12706 -
obs0.229 14118 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.41 Å2 / Biso mean: 60.217 Å2 / Biso min: 41.03 Å2
Refinement stepCycle: final / Resolution: 2.75→59.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 52 7 4315
Biso mean--53.57 53.41 -
Num. residues----539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.850.41771420.324212791421100
2.85-2.960.38931430.318512851428100
2.96-3.090.40281470.281313321479100
3.09-3.260.36131400.257112621402100
3.26-3.460.31751320.23791180131292
3.46-3.730.34561300.23891169129989
3.73-4.10.29021340.22341205133993
4.1-4.70.24911450.181313071452100
4.7-5.920.23131480.208513271475100
5.92-59.860.22071510.18231360151199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.15120.50050.49861.22810.25841.30830.0195-0.13370.0407-0.18260.03670.0238-0.12760.00510.00010.3780.0044-0.00040.4709-0.01690.373924.346-6.34815.131
21.65630.5691-0.01721.0118-0.27831.30990.1301-0.3331-0.10490.1084-0.1578-0.03810.05240.0550.00010.3866-0.0647-0.01760.70330.02060.4327-8.779-24.54929.405
30.00390.0019-0.00480.0133-0.00540.00080.04810.06890.1899-0.33140.33660.2945-0.2004-0.07050.00250.5324-0.02720.02120.8113-0.00340.41814.008-3.865.774
40.0120.0055-0.0070.0154-0.01950.059-0.1177-0.0457-0.02370.0013-0.2393-0.2283-0.1294-0.0678-0.00080.68710.042-0.04210.6762-0.03040.7543-3.927-31.31819.436
50.10110.0184-0.11430.0262-0.00040.14550.162-0.0722-0.00050.0002-0.14050.31610.1597-0.0488-0.00150.71870.08260.03420.71360.14390.529316.613-7.72217.137
60.29890.13320.0720.08160.0370.0189-0.09780.0027-0.0252-0.1165-0.2260.11930.03690.05030.00030.64240.0265-0.15950.91740.11180.5484-1.544-21.91226.649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 54:318 )A54 - 318
2X-RAY DIFFRACTION2( CHAIN B AND RESID 55:318 )B55 - 318
3X-RAY DIFFRACTION3( CHAIN C AND RESID -3:3 )C-3 - 3
4X-RAY DIFFRACTION4( CHAIN D AND RESID -3:2 )D-3 - 2
5X-RAY DIFFRACTION5( CHAIN A AND RESID 401:401 )A401
6X-RAY DIFFRACTION6( CHAIN B AND RESID 401:401 )B401

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