[English] 日本語
Yorodumi
- PDB-8h0n: Crystal structure of the human METTL1-WDR4 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h0n
TitleCrystal structure of the human METTL1-WDR4 complex
Components
  • tRNA (guanine-N(7)-)-methyltransferase
  • tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
KeywordsTRANSFERASE
Function / homology
Function and homology information


internal mRNA (guanine-N7-)-methyltransferase activity / tRNA stabilization / tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase activator activity / tRNA methyltransferase complex / tRNA modification in the nucleus and cytosol ...internal mRNA (guanine-N7-)-methyltransferase activity / tRNA stabilization / tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase activator activity / tRNA methyltransferase complex / tRNA modification in the nucleus and cytosol / tRNA methylation / tRNA modification / enzyme activator activity / Transferases; Transferring one-carbon groups; Methyltransferases / chromosome / tRNA binding / DNA damage response / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit / tRNA (guanine-N-7) methyltransferase catalytic subunit Trm8, eukaryote / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit / tRNA (guanine-N-7) methyltransferase catalytic subunit Trm8, eukaryote / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 / tRNA (guanine-N(7)-)-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJin, X.H. / Guan, Z.Y. / Gong, Z. / Zhang, D.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2017YFD0200400 China
CitationJournal: Cell Discov / Year: 2023
Title: Structural insight into how WDR4 promotes the tRNA N7-methylguanosine methyltransferase activity of METTL1.
Authors: Jin, X. / Guan, Z. / Hu, N. / He, C. / Yin, P. / Gong, Z. / Zhang, D.
History
DepositionSep 30, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
B: tRNA (guanine-N(7)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)68,5792
Polymers68,5792
Non-polymers00
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-5 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.465, 87.030, 95.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 / Protein Wuho homolog / hWH / WD repeat-containing protein 4


Mass: 40359.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P57081
#2: Protein tRNA (guanine-N(7)-)-methyltransferase / Methyltransferase-like protein 1 / mRNA (guanine-N(7)-)-methyltransferase / miRNA (guanine-N(7)-)- ...Methyltransferase-like protein 1 / mRNA (guanine-N(7)-)-methyltransferase / miRNA (guanine-N(7)-)-methyltransferase / tRNA (guanine(46)-N(7))-methyltransferase / tRNA(m7G46)-methyltransferase


Mass: 28219.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL1, C12orf1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UBP6, tRNA (guanine46-N7)-methyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris, Lithium sulphate, PEG3350.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. obs: 66185 / % possible obs: 99.91 % / Redundancy: 2 % / Biso Wilson estimate: 22.67 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.02884 / Rpim(I) all: 0.02884 / Rrim(I) all: 0.04079 / Net I/σ(I): 15.03
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1105 / Mean I/σ(I) obs: 5.57 / Num. unique obs: 13017 / CC1/2: 0.976 / CC star: 0.994 / Rpim(I) all: 0.1105 / Rrim(I) all: 0.1563 / % possible all: 99.98

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IL2

5il2


Resolution: 1.8→38.68 Å / SU ML: 0.1875 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8396
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 3203 4.84 %
Rwork0.1932 62982 -
obs0.1948 66185 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4251 0 0 500 4751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614356
X-RAY DIFFRACTIONf_angle_d0.84915909
X-RAY DIFFRACTIONf_chiral_restr0.0591654
X-RAY DIFFRACTIONf_plane_restr0.0069758
X-RAY DIFFRACTIONf_dihedral_angle_d13.89781567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.23461360.212628X-RAY DIFFRACTION98.5
1.83-1.850.25211580.21392687X-RAY DIFFRACTION99.93
1.85-1.880.26131450.20632712X-RAY DIFFRACTION99.97
1.88-1.920.26881470.21872701X-RAY DIFFRACTION99.96
1.92-1.950.22371220.20912700X-RAY DIFFRACTION100
1.95-1.990.21831250.1982751X-RAY DIFFRACTION99.97
1.99-2.030.23751150.18882721X-RAY DIFFRACTION99.96
2.03-2.070.2261230.18572717X-RAY DIFFRACTION99.93
2.07-2.120.2431250.18562745X-RAY DIFFRACTION99.97
2.12-2.180.25621610.19472715X-RAY DIFFRACTION100
2.18-2.230.22181630.19282688X-RAY DIFFRACTION100
2.23-2.30.18271380.18772709X-RAY DIFFRACTION99.96
2.3-2.370.23581460.18762718X-RAY DIFFRACTION99.97
2.37-2.460.22271420.18972742X-RAY DIFFRACTION99.97
2.46-2.560.23951310.19612728X-RAY DIFFRACTION99.97
2.56-2.670.23631220.19392754X-RAY DIFFRACTION100
2.67-2.810.23151540.20182753X-RAY DIFFRACTION100
2.81-2.990.22091330.1952737X-RAY DIFFRACTION99.97
2.99-3.220.24131260.20132798X-RAY DIFFRACTION100
3.22-3.550.21311610.18652741X-RAY DIFFRACTION99.83
3.55-4.060.21371500.17562781X-RAY DIFFRACTION100
4.06-5.110.20521500.17232805X-RAY DIFFRACTION99.83
5.11-38.680.24691300.22362951X-RAY DIFFRACTION99.23
Refinement TLS params.Method: refined / Origin x: -23.4211915498 Å / Origin y: -2.19971051598 Å / Origin z: 19.0713524516 Å
111213212223313233
T0.156155318478 Å2-0.000825915899647 Å20.0103610824201 Å2-0.16449931191 Å20.00908888202177 Å2--0.139152473517 Å2
L0.180824029567 °2-0.238519047399 °20.0556618075933 °2-0.809055590067 °2-0.0763155039475 °2--0.0357184006626 °2
S0.0344661361215 Å °0.00474759805939 Å °0.00323688377145 Å °-0.0257852634795 Å °-0.0413052566648 Å °-0.115854240936 Å °-0.0215704741445 Å °-0.014730882525 Å °0.000240659900032 Å °
Refinement TLS groupSelection details: all

+
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