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- PDB-7vf2: Human m6A-METTL associated complex (WTAP, VIRMA, ZC3H13, and HAKAI) -

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Basic information

Entry
Database: PDB / ID: 7vf2
TitleHuman m6A-METTL associated complex (WTAP, VIRMA, ZC3H13, and HAKAI)
Components
  • Pre-mRNA-splicing regulator WTAP
  • Protein virilizer homolog
  • Zinc finger CCCH domain-containing protein 13
KeywordsRNA BINDING PROTEIN / m6A-METTL associated complex / cryo-EM / WTAP / Virma.
Function / homology
Function and homology information


regulation of stem cell population maintenance / RNA N6-methyladenosine methyltransferase complex / mRNA alternative polyadenylation / : / regulation of alternative mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA splicing / mRNA processing / nuclear membrane / nuclear body ...regulation of stem cell population maintenance / RNA N6-methyladenosine methyltransferase complex / mRNA alternative polyadenylation / : / regulation of alternative mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA splicing / mRNA processing / nuclear membrane / nuclear body / nuclear speck / cell cycle / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Protein virilizer / Virilizer, N-terminal / Virilizer, N-terminal / Pre-mRNA-splicing regulator WTAP / WTAP/Mum2p family / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Armadillo-type fold
Similarity search - Domain/homology
Pre-mRNA-splicing regulator WTAP / Zinc finger CCCH domain-containing protein 13 / Protein virilizer homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsSu, S. / Li, S. / Deng, T. / Gao, M. / Yin, Y. / Wu, B. / Peng, C. / Liu, J. / Ma, J. / Zhang, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31971130 China
CitationJournal: Cell Res / Year: 2022
Title: Cryo-EM structures of human mA writer complexes.
Authors: Shichen Su / Shanshan Li / Ting Deng / Minsong Gao / Yue Yin / Baixing Wu / Chao Peng / Jianzhao Liu / Jinbiao Ma / Kaiming Zhang /
Abstract: N-methyladenosine (mA) is the most abundant ribonucleotide modification among eukaryotic messenger RNAs. The mA "writer" consists of the catalytic subunit mA-METTL complex (MAC) and the regulatory ...N-methyladenosine (mA) is the most abundant ribonucleotide modification among eukaryotic messenger RNAs. The mA "writer" consists of the catalytic subunit mA-METTL complex (MAC) and the regulatory subunit mA-METTL-associated complex (MACOM), the latter being essential for enzymatic activity. Here, we report the cryo-electron microscopy (cryo-EM) structures of MACOM at a 3.0-Å resolution, uncovering that WTAP and VIRMA form the core structure of MACOM and that ZC3H13 stretches the conformation by binding VIRMA. Furthermore, the 4.4-Å resolution cryo-EM map of the MACOM-MAC complex, combined with crosslinking mass spectrometry and GST pull-down analysis, elucidates a plausible model of the mA writer complex, in which MACOM binds to MAC mainly through WTAP and METTL3 interactions. In combination with in vitro RNA substrate binding and mA methyltransferase activity assays, our results illustrate the molecular basis of how MACOM assembles and interacts with MAC to form an active mA writer complex.
History
DepositionSep 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein virilizer homolog
B: Zinc finger CCCH domain-containing protein 13
C: Pre-mRNA-splicing regulator WTAP
D: Pre-mRNA-splicing regulator WTAP


Theoretical massNumber of molelcules
Total (without water)355,1094
Polymers355,1094
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area30580 Å2
ΔGint-238 kcal/mol
Surface area69990 Å2

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Components

#1: Protein Protein virilizer homolog


Mass: 202244.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VIRMA, KIAA1429, MSTP054 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q69YN4
#2: Protein Zinc finger CCCH domain-containing protein 13


Mass: 64277.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZC3H13, KIAA0853 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5T200
#3: Protein Pre-mRNA-splicing regulator WTAP / Female-lethal(2)D homolog / hFL(2)D / WT1-associated protein / Wilms tumor 1-associating protein


Mass: 44293.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WTAP, KIAA0105 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15007

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human m6A-METTL associated complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
2EPU2.9image acquisition
13cryoSPARC3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 395916 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413766
ELECTRON MICROSCOPYf_angle_d0.61718594
ELECTRON MICROSCOPYf_dihedral_angle_d7.3518587
ELECTRON MICROSCOPYf_chiral_restr0.042186
ELECTRON MICROSCOPYf_plane_restr0.0042392

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