[English] 日本語
Yorodumi
- PDB-7yf4: Crystal structure of METTL9 in complex with SLC39A5 mutant peptid... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more