+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31947 | |||||||||
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Title | Human m6A-METTL associated complex (WTAP, VIRMA, and HAKAI) | |||||||||
Map data | Human m6A-METTL associated complex(WTAP, VIRMA,and HAKAI) | |||||||||
Sample |
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Keywords | m6A-METTL associated complex / cryo-EM / WTAP / Virma. / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information 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 body / nuclear speck / RNA binding ...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 body / nuclear speck / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Su S / Li S | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31947.map.gz | 136.3 MB | EMDB map data format | |
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Header (meta data) | emd-31947-v30.xml emd-31947.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_31947.png | 82.1 KB | ||
Filedesc metadata | emd-31947.cif.gz | 6.5 KB | ||
Others | emd_31947_additional_1.map.gz | 72.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31947 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31947 | HTTPS FTP |
-Validation report
Summary document | emd_31947_validation.pdf.gz | 482.2 KB | Display | EMDB validaton report |
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Full document | emd_31947_full_validation.pdf.gz | 481.8 KB | Display | |
Data in XML | emd_31947_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_31947_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31947 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31947 | HTTPS FTP |
-Related structure data
Related structure data | 7vf5MC 7vf2C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31947.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Human m6A-METTL associated complex(WTAP, VIRMA,and HAKAI) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unmasked Map
File | emd_31947_additional_1.map | ||||||||||||
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Annotation | Unmasked Map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human m6A-METTL associated complex(HWV)
Entire | Name: Human m6A-METTL associated complex(HWV) |
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Components |
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-Supramolecule #1: Human m6A-METTL associated complex(HWV)
Supramolecule | Name: Human m6A-METTL associated complex(HWV) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Protein virilizer homolog
Macromolecule | Name: Protein virilizer homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 202.2445 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Macromolecule #2: Pre-mRNA-splicing regulator WTAP
Macromolecule | Name: Pre-mRNA-splicing regulator WTAP / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.293531 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied 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: 282821 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |