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- EMDB-33807: Structure of WTAP-VIRMA in the m6A writer complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33807
TitleStructure of WTAP-VIRMA in the m6A writer complex
Map data
Sample
  • Complex: WTAP-VIRMA complex
    • Protein or peptide: Protein virilizer homolog
    • Protein or peptide: Pre-mRNA-splicing regulator WTAP
KeywordsPROTEIN BINDING
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 speck / nuclear body / 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 speck / nuclear body / RNA 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 / Armadillo-type fold
Similarity search - Domain/homology
Pre-mRNA-splicing regulator WTAP / Protein virilizer homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYan XH / Guan ZY / Tang C / Yin P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionJul 11, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33807.png

Downloads & links

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Map

FileDownload / File: emd_33807.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1365722 - 2.3653538
Average (Standard dev.)0.001196644 (±0.048114426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33807_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33807_half_map_2.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 : WTAP-VIRMA complex

EntireName: WTAP-VIRMA complex
Components
  • Complex: WTAP-VIRMA complex
    • Protein or peptide: Protein virilizer homolog
    • Protein or peptide: Pre-mRNA-splicing regulator WTAP

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Supramolecule #1: WTAP-VIRMA complex

SupramoleculeName: WTAP-VIRMA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 123.716016 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

UniProtKB: Protein virilizer homolog

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Macromolecule #2: Pre-mRNA-splicing regulator WTAP

MacromoleculeName: Pre-mRNA-splicing regulator WTAP / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.107188 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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

Concentration0.4 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 197685
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.2)
Final 3D classificationSoftware - Name: cryoSPARC

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