+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33807 | |||||||||
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Title | Structure of WTAP-VIRMA in the m6A writer complex | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information 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 ...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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Yan XH / Guan ZY / Tang C / Yin P | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2022 Title: AI-empowered integrative structural characterization of mA methyltransferase complex. Authors: Xuhui Yan / Kai Pei / Zeyuan Guan / Feiqing Liu / Junjun Yan / Xiaohuan Jin / Qiang Wang / Mengjun Hou / Chun Tang / Ping Yin / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33807.map.gz | 79.1 MB | EMDB map data format | |
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Header (meta data) | emd-33807-v30.xml emd-33807.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
Images | emd_33807.png | 45.1 KB | ||
Others | emd_33807_half_map_1.map.gz emd_33807_half_map_2.map.gz | 77.6 MB 77.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33807 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33807 | HTTPS FTP |
-Related structure data
Related structure data | 7yg4MC 7yfjC M: atomic model generated by this map C: citing same article (ref.) |
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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_33807.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33807_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33807_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : WTAP-VIRMA complex
Entire | Name: WTAP-VIRMA complex |
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Components |
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-Supramolecule #1: WTAP-VIRMA complex
Supramolecule | Name: WTAP-VIRMA complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-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: 123.716016 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MASVKLTELL DLYREDRGAK WVTALEEIPS LIIKGLSYLQ LKNTKQDSLG QLVDWTMQAL NLQVALRQPI ALNVRQLKAG TKLVSSLAE CGAQGVTGLL QAGVISGLFE LLFADHVSSS LKLNAFKALD SVISMTEGME AFLRGRQNEK SGYQKLLELI L LDQTVRVV ...String: MASVKLTELL DLYREDRGAK WVTALEEIPS LIIKGLSYLQ LKNTKQDSLG QLVDWTMQAL NLQVALRQPI ALNVRQLKAG TKLVSSLAE CGAQGVTGLL QAGVISGLFE LLFADHVSSS LKLNAFKALD SVISMTEGME AFLRGRQNEK SGYQKLLELI L LDQTVRVV TAGSAILQKC HFYEVLSEIK RLGDHLAEKT SSLPNHSEPD HDTDAGLERT NPEYENEVEA SMDMDLLESS NI SEGEIER LINLLEEVFH LMETAPHTMI QQPVKSFPTM ARITGPPERD DPYPVLFRYL HSHHFLELVT LLLSIPVTSA HPG VLQATK DVLKFLAQSQ KGLLFFMSEY EATNLLIRAL CHFYDQDEEE GLQSDGVIDD AFALWLQDST QTLQCITELF SHFQ RCTAS EETDHSDLLG TLHNLYLITF NPVGRSAVGH VFSLEKNLQS LITLMEYYSK EALGDSKSKK SVAYNYACIL ILVVV QSSS DVQMLEQHAA SLLKLCKADE NNAKLQELGK WLEPLKNLRF EINCIPNLIE YVKQNIDNLM TPEGVGLTTA LRVLCN VAC PPPPVEGQQK DLKWNLAVIQ LFSAEGMDTF IRVLQKLNSI LTQPWRLHVN MGTTLHRVTT ISMARCTLTL LKTMLTE LL RGGSFEFKDM RVPSALVTLH MLLCSIPLSG RLDSDEQKIQ NDIIDILLTF TQGVNEKLTI SEETLANNTW SLMLKEVL S SILKVPEGFF SGLILLSELL PLPLPMQTTQ VIEPHDISVA LNTRKLWSMH LHVQAKLLQE IVRSFSGTTC QPIQHMLRR ICVQLCDLAS PTALLIMRTV LDLIVEDLQS TSEDKEKQYT SQTTRLLALL DALASHKACK LAILHLINGT IKGDERYAEI FQDLLALVR SPGDSVIRQQ CVEYVTSILQ SLCDQDIALI LPSSSEGSIS ELEQLSNSLP NKELMTSICD CLLATLANSE S SYNCLLTC VRTMMFLAEH DYGLFHLKSS LRKNSSALHS LLKRVVSTFS KDTGELASSF LEFMRQILNS DTIGCCGDDN GL MEVEGAH TSRTMSINAA ELKQLLQSKE ESPENLFLEL EKLVLEHSKD DDNLDSLLDS VVGLKQMLES |
-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: 34.107188 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MHHHHHHHHH HSGDEVDAGS GHMTNEEPLP KKVRLSETDF KVMARDELIL RWKQYEAYVQ ALEGKYTDLN SNDVTGLRES EEKLKQQQQ ESARRENILV MRLATKEQEM QECTTQIQYL KQVQQPSVAQ LRSTMVDPAI NLFFLKMKGE LEQTKDKLEQ A QNELSAWK ...String: MHHHHHHHHH HSGDEVDAGS GHMTNEEPLP KKVRLSETDF KVMARDELIL RWKQYEAYVQ ALEGKYTDLN SNDVTGLRES EEKLKQQQQ ESARRENILV MRLATKEQEM QECTTQIQYL KQVQQPSVAQ LRSTMVDPAI NLFFLKMKGE LEQTKDKLEQ A QNELSAWK FTPDSQTGKK LMAKCRMLIQ ENQELGRQLS QGRIAQLEAE LALQKKYSEE LKSSQDELND FIIQLDEEVE GM QSTILVL QQQLKETRQQ LAQYQQQQSQ ASAPSTSRTT ASEPVEQSEA TSKDCSRL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.1 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: PROJECTION MATCHING |
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Final 3D classification | Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.2) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 197685 |