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- EMDB-39509: ASFV RNA polymerase-M1249L complex4 -

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Basic information

Entry
Database: EMDB / ID: EMD-39509
TitleASFV RNA polymerase-M1249L complex4
Map data
Sample
  • Complex: African swine fever virus RNA polymerase complex
    • Protein or peptide: DNA-directed RNA polymerase subunit
    • Protein or peptide: D339L
    • Protein or peptide: M1249L
KeywordsASFV / RNA polymerase / VIRAL PROTEIN
Function / homology
Function and homology information


viral transcription / DNA-directed RNA polymerase complex / : / : / : / : / : / : / DNA-directed RNA polymerase / DNA binding
Similarity search - Function
RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 ...RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus
Similarity search - Domain/homology
D339L / M1249L / DNA-directed RNA polymerase subunit
Similarity search - Component
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsFeng XY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Transcription regulation of African swine fever virus: dual role of M1249L.
Authors: Dongming Zhao / Nan Wang / Xiaoying Feng / Zhenjiang Zhang / Kongen Xu / Tao Zheng / Yunge Yang / Xuemei Li / Xianjin Ou / Rui Zhao / Zihe Rao / Zhigao Bu / Yutao Chen / Xiangxi Wang /
Abstract: African swine fever virus (ASFV), which poses significant risks to the global economy, encodes a unique host-independent transcription system. This system comprises an eight-subunit RNA polymerase ...African swine fever virus (ASFV), which poses significant risks to the global economy, encodes a unique host-independent transcription system. This system comprises an eight-subunit RNA polymerase (vRNAP), temporally expressed transcription factors and transcript associated proteins, facilitating cross-species transmission via intermediate host. The protein composition of the virion and the presence of transcription factors in virus genome suggest existence of distinct transcription systems during viral infection. However, the precise mechanisms of transcription regulation remain elusive. Through analyses of dynamic transcriptome, vRNAP-associated components and cell-based assay, the critical role of M1249L in viral transcription regulation has been highlighted. Atomic-resolution structures of vRNAP-M1249L supercomplex, exhibiting a variety of conformations, have uncovered the dual functions of M1249L. During early transcription, M1249L could serve as multiple temporary transcription factors with C-terminal domain acting as a switcher for activation/inactivation, while during late transcription it aids in the packaging of the transcription machinery. The structural and functional characteristics of M1249L underscore its vital roles in ASFV transcription, packaging, and capsid assembly, presenting novel opportunities for therapeutic intervention.
History
DepositionMar 20, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39509.png

Downloads & links

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Map

FileDownload / File: emd_39509.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 360 pix.
= 290.88 Å		0.81 Å/pix.
x 360 pix.
= 290.88 Å		0.81 Å/pix.
x 360 pix.
= 290.88 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.57
Minimum - Maximum-2.92154 - 4.5297556
Average (Standard dev.)0.00069241633 (±0.0842574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 290.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39509_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39509_half_map_2.map
Projections & Slices
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Sample components

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Entire : African swine fever virus RNA polymerase complex

EntireName: African swine fever virus RNA polymerase complex
Components
  • Complex: African swine fever virus RNA polymerase complex
    • Protein or peptide: DNA-directed RNA polymerase subunit
    • Protein or peptide: D339L
    • Protein or peptide: M1249L

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Supramolecule #1: African swine fever virus RNA polymerase complex

SupramoleculeName: African swine fever virus RNA polymerase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: African swine fever virus

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Macromolecule #1: DNA-directed RNA polymerase subunit

MacromoleculeName: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 163.933938 KDa
SequenceString: MEAGYAEIAA VQFNIAGDND HKRQGVMEVT ISNLFEGTLP AEGGIYDARM GTTDHHYKCI TCSHQRKQCM GHPGILQMHA PVLQPLFIA EIRRWLRVIC LNCGAPIVDL KRYEHLIRPK RLIEAASSQT EGKQCYVCKA VHPKIVKDSE DYFTFWADQQ G KIDKLYPQ ...String:
MEAGYAEIAA VQFNIAGDND HKRQGVMEVT ISNLFEGTLP AEGGIYDARM GTTDHHYKCI TCSHQRKQCM GHPGILQMHA PVLQPLFIA EIRRWLRVIC LNCGAPIVDL KRYEHLIRPK RLIEAASSQT EGKQCYVCKA VHPKIVKDSE DYFTFWADQQ G KIDKLYPQ IIREIFSRVT YDTVVKLGRS KNSHPEKLVL KAIQIPPISI RPGIRLGIGS GPQSFHDINN VIQYLVRKNL LI PKDLQIV RGQKIPLNID RNLQTIQQLY YNFLLDSVST TATQGGTGKR GIVMGARPAP SIMRRLPRKE GRIRKSLLGS QVW SISRST ICGNSDLHLD EVGYPISFAR TLQVAETVQH YNINRLMPYF LNGKRQYPGC SRVYKQITQS VHDIEGLKQD FRLE VGDIL YRDVVTGDVA FFNRQPSLER SSIGVHRIVV LENPKISTFQ MNVSACAWYN ADFDGDQMNL WVPWSVMSRV EAELL CSVR NWFISTKSSG PVNGQVQDST VGSFLLTRTN TPMGKNVMNK LHAMGLFQTT QTDPPCFANY SPTDLLDGKS VVSMLL RQT PINYQRAPTW YSEVYAPYMH YNKQDISTQI RNGELIEGVL DKKAVGAGSS GGIYHLISRR YGPQQALKMI FATQQLA LN YVRNAGFTVS TADMLLTPEA HQEVQEIINE LLLESEEINN RLLHGDIMPP IGLTTHDFYE KLQLNALKFP DRILKPIM N SINPETNGLF QMVATGAKGS NPNMIHIMAG IGQIEINTQR IQPQFSFGRT LVYYPRFALE AQAYGFICNS YIAGLTSPE FIFGEMNGRF DLINKALSTS STGYANRKAI FGLQSCIVDY YRRVSIDTRL VQQLYGEDGL DARQLETVRF ETIMLSDQEL EDKFKYTGI QSPLFEEEFS RLKKDRDKYR QIFLNVENFN FSQLLTDVRQ VPVNVASIVK NILLSSTSGV LPFDEKSILQ K YAMVKTFC KNLPYVFINN IQERLQTPIP VYLKRAASLM RMLIRIELAT VKTLNITCEQ MSAILDLIRL QYTQSLINYG EA VGILAAQ SVSEPLTQYM LDSHHRSVAG GTNKSGIVRP QEIFSAKPVE AEQSSEMLLR LKNPEVETNK TYAQEIANSI ELI TFERLI LQWHLLYETY SSTKKNVMYP DFASDVEWMT DFLENHPLLQ PPEDIANWCI RLELNKTTMI LKSISLESII NSLR AKHPN TYIMHSVENT ASGIPIIIRI YLRESAFRRS TNTRMATDEK IAVNVVDKLL NSTIRGIPGI KNANVVKLMR HRVDA QGKL VRLDNIYAIK TNGTNIFGAM LDDNIDPYTI VSSSIGDTME LYGIEAARQK IISEIRTVMG DKGPNHRHLL MYADLM TRT GQVTSLEKAG LNAREPSNVL LRMALSSPVQ VLTDAAVDSA VNPIYGIAAP TLMGSVPRIG TMYSDIIMDE KYITENY KS VDSLIDML

UniProtKB: DNA-directed RNA polymerase subunit

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Macromolecule #2: D339L

MacromoleculeName: D339L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 38.798594 KDa
SequenceString: MIDQKIFETT LNIDDPTNFC TNVEAHLLKE LENIYVGKCF KNSFILNITG VIQRSPCFIM RTNNSGRGYM HVRFSAVVSY LNAFDLIAA VKIIKNDSNI ILGESLLTEP VTIVIPSSES QNNVAEVGQI VPVQLANSSV YYIPGRQQAS ATGSIFIPKH T FSVYHVQE ...String:
MIDQKIFETT LNIDDPTNFC TNVEAHLLKE LENIYVGKCF KNSFILNITG VIQRSPCFIM RTNNSGRGYM HVRFSAVVSY LNAFDLIAA VKIIKNDSNI ILGESLLTEP VTIVIPSSES QNNVAEVGQI VPVQLANSSV YYIPGRQQAS ATGSIFIPKH T FSVYHVQE ELTQEQALNL TKLVNIIEML LESRSKKDFK QICFFEKLYY TYSISSDEIL DLKIWKGPKG KEMSRLKPCN VL SFLYDAL KNKNSSLGFW ARPPNLLKSS PLAYQQDQNS FNATELPIIC SAEVMFVTLL KEIINYLQFI NDLCDTFNNE QLI KRHENI WMLIEQRKIG HDF

UniProtKB: D339L

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Macromolecule #3: M1249L

MacromoleculeName: M1249L / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 144.604125 KDa
SequenceString: MEEVITIAQI VHRGTDILSL NNEEIEALVD EIYSTLKGSN DIKNIRLIDF LFTLKDFVNH VRAEQSKLPD LSMPIEAYIR QLLVDPDVV PIVSEKKKEL RVRPSTRKEI FLINGTHLAV PAEAPIEIYG LKLRLKTFSP QCFMRMAEIG SFSPETLGYV A SGANLTNF ...String:
MEEVITIAQI VHRGTDILSL NNEEIEALVD EIYSTLKGSN DIKNIRLIDF LFTLKDFVNH VRAEQSKLPD LSMPIEAYIR QLLVDPDVV PIVSEKKKEL RVRPSTRKEI FLINGTHLAV PAEAPIEIYG LKLRLKTFSP QCFMRMAEIG SFSPETLGYV A SGANLTNF IRVFMKCVDQ ETWKKNGEGV VVTTKENIIQ FTHQYIELYK FLRSGGHSWL INRLAEEMVH RKLDREDQGS HI SNIVETE EIEPEENIKR VIFFLKELST MYSVSPVFTS GYMPLLYDLY RAGYLEVLWN PVEQKFLQHA EQREKEQMIL QQV DMKLTE VITQARQYFK IMEEKIGRVQ SDAIREILTM EGKVDDPNSI LQEVIKACGK QEAELITTEY LNIKKQWELQ EKNA CAHLK LVKQLRSGLQ YAELLKVLES IRVLYKEKNN TTNWNLCKAC GFKLLCPHVD MLIQLQAAEA SYDTMRTKLM KFSGI NKEK ENNQGLIYSY FCKICGEELA HFIQEDRTAD VGIIGDLNSK LRVFIWQETM KACTFIHFGK LVDVKQFANI AVNVCL PLV YSIENIKKEE DYDPLTQLYA VIYIYAYILN LIYSSQKNKE FLTITIHGMK ADSSLNAYVT FLLEKMMQQY SGIINQL SE ITDQWIANNF REAFKKIIHQ NGLQGLSVQD DTKVLLTEIL LDPMYDYAAT VARIDGSIPM HKPRTPKEAE YEFKTVIG R TPAELLSQKE FYDKIYTSKY RPDFTQLTRL NDIYFQEESL RVWWGGRDEE KTSTLIYLRA YELFLKYLQN APNFNSELA EFKTYENAYG EQKALLAQQG FYNIFDPNTG RADQRTRLFE YKRLPISTLY DERGLPHKWT IYVYKAVDSS QKPAEIEVTR KDVIKKIDN HYALADLRCS VCHVLQHEVG QLNIKKVQTA LKASLEFNTF YAFYESRCPK GGLHDFQDKK CVKCGLFTYI I YDHLSQPE LVHDYYNNYK DQYDKEKMSI RSIQIKKDMT TPSTETQPKP PQEPWTFDYG KIIKTAKILD ISPAVIEAIG AM EGRSYAD IREGQGAPPP PTSMDDPRLM AVDSAVRIFL YNYNCLRHVS TFNKPPIHVE RLVKHLSYEE KEDLEKVLPN VVN EYHTTF KHLRVTDPAS ALLYSIEFLC ISFLTLYEIK EPSWVVNIVR EFALTELNTI IQSEKLLSKP GAFNFMIFGE DFVC SGEDS SMDDISAYSS PGLFGEDIID RLDDPFSIED VDISLDVLDN LAPQ

UniProtKB: M1249L

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 218831
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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