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- PDB-7yf2: Crystal structure of METTL9 in complex with unmethylated SLC39A5 ... -

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Basic information

Entry
Database: PDB / ID: 7yf2
TitleCrystal structure of METTL9 in complex with unmethylated SLC39A5 peptide and SAH
Components
  • Protein-L-histidine N-pros-methyltransferase
  • SLC39A5 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: 1.691 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 1.1Apr 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 peptide
D: SLC39A5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6026
Polymers65,8334
Non-polymers7692
Water8,215456
1
A: Protein-L-histidine N-pros-methyltransferase
C: SLC39A5 peptide
hetero molecules

B: Protein-L-histidine N-pros-methyltransferase
D: SLC39A5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6026
Polymers65,8334
Non-polymers7692
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area4660 Å2
ΔGint-28 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.838, 45.836, 106.415
Angle α, β, γ (deg.)90.000, 122.640, 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 peptide


Mass: 1362.371 Da / Num. of mol.: 2
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.: 456 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BICINE pH 9.0, 2% 1,4-Dioxane, 10% w/v PEG 20000, 12% Glycerol, 0.01 M TCEP

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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: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.69→60.56 Å / Num. obs: 63898 / % possible obs: 97.4 % / Redundancy: 5.6 % / CC1/2: 0.999 / Net I/σ(I): 16
Reflection shellResolution: 1.69→1.78 Å / Num. unique obs: 63898 / CC1/2: 0.892

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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: Model from alphaFold2

Resolution: 1.691→35.418 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 1999 3.13 %
Rwork0.1792 61899 -
obs0.1804 63898 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.26 Å2 / Biso mean: 32.9245 Å2 / Biso min: 12.78 Å2
Refinement stepCycle: final / Resolution: 1.691→35.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 52 456 5038
Biso mean--23.46 38.23 -
Num. residues----567
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.691-1.73330.31291220.2545380585
1.7333-1.78010.26931390.2379427194
1.7801-1.83250.26151450.217448899
1.8325-1.89170.24991440.2108445799
1.8917-1.95930.25051430.206443399
1.9593-2.03770.23791440.1992446998
2.0377-2.13040.2221420.1905441898
2.1304-2.24280.22891450.1886449399
2.2428-2.38320.21211460.1878448699
2.3832-2.56720.23111430.1958444398
2.5672-2.82550.2191460.1918451199
2.8255-3.23410.21011450.1801449498
3.2341-4.07360.21951460.1534453899
4.0736-35.4180.1821490.1561459397
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)
11.25560.4121-0.17050.8827-0.03320.90230.0280.00810.14190.01570.02260.0031-0.06280.0171-0.0440.15140.0104-0.0050.1314-0.01120.154724.5436-6.324614.7364
22.83780.9367-0.89511.512-0.6341.57480.2358-0.60340.04410.331-0.2154-0.007-0.14730.162-0.00740.2034-0.0543-0.0080.25610.00470.160363.2177-3.496729.7166
30.3620.3186-0.5062.0902-0.78370.78230.05790.30120.7896-0.3495-0.04780.6685-0.3228-0.23720.09210.23630.038-0.0260.25720.04690.382615.289-0.67946.074
40.41010.5909-0.25441.1169-0.58920.3633-0.3403-0.3589-0.7526-0.1457-0.2661-0.52340.61650.41810.54810.33020.07560.05360.32840.13140.382367.9382-13.956421.6016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 44 through 401)A44 - 401
2X-RAY DIFFRACTION2(chain 'B' and resid 51 through 401)B51 - 401
3X-RAY DIFFRACTION3(chain 'C' and resid -4 through 7)C-4 - 7
4X-RAY DIFFRACTION4(chain 'D' and resid -4 through 7)D-4 - 7

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