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- EMDB-31946: Human m6A-METTL associated complex (WTAP, VIRMA, ZC3H13, and HAKAI) -

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Basic information

Entry
Database: EMDB / ID: EMD-31946
TitleHuman m6A-METTL associated complex (WTAP, VIRMA, ZC3H13, and HAKAI)
Map dataHuman m6A-METTL associated complex(WTAP, VIRMA, ZC3H13, and HAKAI)
Sample
  • Complex: Human m6A-METTL associated complex
    • Protein or peptide: Protein virilizer homolog
    • Protein or peptide: Zinc finger CCCH domain-containing protein 13
    • Protein or peptide: Pre-mRNA-splicing regulator WTAP
Keywordsm6A-METTL associated complex / cryo-EM / WTAP / Virma. / RNA BINDING PROTEIN
Function / homology
Function and homology information


regulation of stem cell population maintenance / RNA N6-methyladenosine methyltransferase complex / mRNA modification / regulation of alternative mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA splicing / mRNA processing / nuclear membrane / nuclear speck / nuclear body ...regulation of stem cell population maintenance / RNA N6-methyladenosine methyltransferase complex / mRNA modification / regulation of alternative mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA splicing / mRNA processing / nuclear membrane / nuclear speck / nuclear body / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / 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 ...: / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSu S / Li S
Funding support China, 1 items
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, 2021-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31946.png

Downloads & links

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Map

FileDownload / File: emd_31946.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman m6A-METTL associated complex(WTAP, VIRMA, ZC3H13, and HAKAI)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-1.5568033 - 2.8558378
Average (Standard dev.)0.00511443 (±0.07024383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 275.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unmasked map

Fileemd_31946_additional_1.map
AnnotationUnmasked map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human m6A-METTL associated complex

EntireName: Human m6A-METTL associated complex
Components
  • Complex: Human m6A-METTL associated complex
    • Protein or peptide: Protein virilizer homolog
    • Protein or peptide: Zinc finger CCCH domain-containing protein 13
    • Protein or peptide: Pre-mRNA-splicing regulator WTAP

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Supramolecule #1: Human m6A-METTL associated complex

SupramoleculeName: Human m6A-METTL associated complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Protein virilizer homolog

MacromoleculeName: Protein virilizer homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 202.2445 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAVDSAMELL FLDTFKHPSA EQSSHIDVVR FPCVVYINEV RVIPPGVRAH SSLPDNRAYG ETSPHTFQLD LFFNNVSKPS APVFDRLGS LEYDENTSII FRPNSKVNTD GLVLRGWYNC LTLAIYGSVD RVISHDRDSP PPPPPPPPPP QPQPSLKRNP K HADGEKED ...String:
MAVDSAMELL FLDTFKHPSA EQSSHIDVVR FPCVVYINEV RVIPPGVRAH SSLPDNRAYG ETSPHTFQLD LFFNNVSKPS APVFDRLGS LEYDENTSII FRPNSKVNTD GLVLRGWYNC LTLAIYGSVD RVISHDRDSP PPPPPPPPPP QPQPSLKRNP K HADGEKED QFNGSPPRPQ PRGPRTPPGP PPPDDDEDDP VPLPVSGDKE EDAPHREDYF EPISPDRNSV PQEGQYSDEG EV EEEQQEE GEEDEDDVDV EEEEDEDEDD RRTVDSIPEE EEEDEEEEGE EDEEGEGDDG YEQISSDEDG IADLERETFK YPN FDVEYT AEDLASVPPM TYDPYDRELV PLLYFSCPYK TTFEIEISRM KDQGPDKENS GAIEASVKLT ELLDLYREDR GAKW VTALE EIPSLIIKGL SYLQLKNTKQ DSLGQLVDWT MQALNLQVAL RQPIALNVRQ LKAGTKLVSS LAECGAQGVT GLLQA GVIS GLFELLFADH VSSSLKLNAF KALDSVISMT EGMEAFLRGR QNEKSGYQKL LELILLDQTV RVVTAGSAIL QKCHFY EVL SEIKRLGDHL AEKTSSLPNH SEPDHDTDAG LERTNPEYEN EVEASMDMDL LESSNISEGE IERLINLLEE VFHLMET AP HTMIQQPVKS FPTMARITGP PERDDPYPVL FRYLHSHHFL ELVTLLLSIP VTSAHPGVLQ ATKDVLKFLA QSQKGLLF F MSEYEATNLL IRALCHFYDQ DEEEGLQSDG VIDDAFALWL QDSTQTLQCI TELFSHFQRC TASEETDHSD LLGTLHNLY LITFNPVGRS AVGHVFSLEK NLQSLITLME YYSKEALGDS KSKKSVAYNY ACILILVVVQ SSSDVQMLEQ HAASLLKLCK ADENNAKLQ ELGKWLEPLK NLRFEINCIP NLIEYVKQNI DNLMTPEGVG LTTALRVLCN VACPPPPVEG QQKDLKWNLA V IQLFSAEG MDTFIRVLQK LNSILTQPWR LHVNMGTTLH RVTTISMARC TLTLLKTMLT ELLRGGSFEF KDMRVPSALV TL HMLLCSI PLSGRLDSDE QKIQNDIIDI LLTFTQGVNE KLTISEETLA NNTWSLMLKE VLSSILKVPE GFFSGLILLS ELL PLPLPM QTTQVIEPHD ISVALNTRKL WSMHLHVQAK LLQEIVRSFS GTTCQPIQHM LRRICVQLCD LASPTALLIM RTVL DLIVE DLQSTSEDKE KQYTSQTTRL LALLDALASH KACKLAILHL INGTIKGDER YAEIFQDLLA LVRSPGDSVI RQQCV EYVT SILQSLCDQD IALILPSSSE GSISELEQLS NSLPNKELMT SICDCLLATL ANSESSYNCL LTCVRTMMFL AEHDYG LFH LKSSLRKNSS ALHSLLKRVV STFSKDTGEL ASSFLEFMRQ ILNSDTIGCC GDDNGLMEVE GAHTSRTMSI NAAELKQ LL QSKEESPENL FLELEKLVLE HSKDDDNLDS LLDSVVGLKQ MLESSGDPLP LSDQDVEPVL SAPESLQNLF NNRTAYVL A DVMDDQLKSM WFTPFQAEEI DTDLDLVKVD LIELSEKCCS DFDLHSELER SFLSEPSSPG RTKTTKGFKL GKHKHETFI TSSGKSEYIE PAKRAHVVPP PRGRGRGGFG QGIRPHDIFR QRKQNTSRPP SMHVDDFVAA ESKEVVPQDG IPPPKRPLKV SQKISSRGG FSGNRGGRGA FHSQNRFFTP PASKGNYSRR EGTRGSSWSA QNTPRGNYNE SRGGQSNFNR GPLPPLRPLS S TGYRPSPR DRASRGRGGL GPSWASANSG SGGSRGKFVS GGSGRGRHVR SFTR

UniProtKB: Protein virilizer homolog

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Macromolecule #2: Zinc finger CCCH domain-containing protein 13

MacromoleculeName: Zinc finger CCCH domain-containing protein 13 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.277785 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: PVATATATTV PATLAATTAA AATSFSTSAI TISTSATPTN TTNNTFANED SHRKCHRTRV EKVETPHVTI EDAQHRKPMD QKRSSSLGS NRSNRSHTSG RLRSPSNDSA HRSGDDQSGR KRVLHSGSRD REKTKSLEIT GERKSRIDQL KRGEPSRSTS S DRQDSRSH ...String:
PVATATATTV PATLAATTAA AATSFSTSAI TISTSATPTN TTNNTFANED SHRKCHRTRV EKVETPHVTI EDAQHRKPMD QKRSSSLGS NRSNRSHTSG RLRSPSNDSA HRSGDDQSGR KRVLHSGSRD REKTKSLEIT GERKSRIDQL KRGEPSRSTS S DRQDSRSH SSRRSSPESD RQVHSRSGSF DSRDRLQERD RYEHDRERER ERRDTRQREW DRDADKDWPR NRDRDRLRER ER ERERDKR RDLDRERERL ISDSVERDRD RDRDRTFESS QIESVKRCEA KLEGEHERDL ESTSRDSLAL DKERMDKDLG SVQ GFEETN KSERTESLEG DDESKLDDAH SLGSGAGEGY EPISDDELDE ILAGDAEKRE DQQDEEKMPD PLDVIDVDWS GLMP KHPKE PREPGAALLK FTPGAVMLRV GISKKLAGSE LFAKVKETCQ RLLEKPKDAD NLFEHELGAL NMAALLRKEE RASLL SNLG PCCKALCFRR DSAIRKQLVK NEKGTIKQAY TSAPMVDNEL LRLSLRLFKR KTTCHAPGHE KTEDNKLSQS SIQQEL CVS

UniProtKB: Zinc finger CCCH domain-containing protein 13

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Macromolecule #3: Pre-mRNA-splicing regulator WTAP

MacromoleculeName: Pre-mRNA-splicing regulator WTAP / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.293531 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTNEEPLPKK VRLSETDFKV MARDELILRW KQYEAYVQAL EGKYTDLNSN DVTGLRESEE KLKQQQQESA RRENILVMRL ATKEQEMQE CTTQIQYLKQ VQQPSVAQLR STMVDPAINL FFLKMKGELE QTKDKLEQAQ NELSAWKFTP DSQTGKKLMA K CRMLIQEN ...String:
MTNEEPLPKK VRLSETDFKV MARDELILRW KQYEAYVQAL EGKYTDLNSN DVTGLRESEE KLKQQQQESA RRENILVMRL ATKEQEMQE CTTQIQYLKQ VQQPSVAQLR STMVDPAINL FFLKMKGELE QTKDKLEQAQ NELSAWKFTP DSQTGKKLMA K CRMLIQEN QELGRQLSQG RIAQLEAELA LQKKYSEELK SSQDELNDFI IQLDEEVEGM QSTILVLQQQ LKETRQQLAQ YQ QQQSQAS APSTSRTTAS EPVEQSEATS KDCSRLTNGP SNGSSSRQRT SGSGFHREGN TTEDDFPSSP GNGNKSSNSS EER TGRGGS GYVNQLSAGY ESVDSPTGSE NSLTHQSNDT DSSHDPQEEK AVSGKGNRTV GSRHVQNGLD SSVNVQGSVL

UniProtKB: Pre-mRNA-splicing regulator WTAP

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 395916
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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