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- EMDB-60755: Cryo-EM structure of the RNA-dependent RNA polymerase complex fro... -

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Basic information

Entry
Database: EMDB / ID: EMD-60755
TitleCryo-EM structure of the RNA-dependent RNA polymerase complex from Marburg virus
Map data
Sample
  • Complex: Ternary complex of L-VP35 from Marburg virus
    • Protein or peptide: RNA-directed RNA polymerase L,Maltose/maltodextrin-binding periplasmic protein
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35
  • Ligand: ZINC ION
KeywordsRNA-dependent RNA polymerase complex / VIRAL PROTEIN
Function / homology
Function and homology information


negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / detection of maltose stimulus / maltose transport complex / carbohydrate transport / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / carbohydrate transmembrane transporter activity / maltose binding ...negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / detection of maltose stimulus / maltose transport complex / carbohydrate transport / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / membrane scission GTPase motor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / periplasmic space / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / DNA damage response / ATP binding / membrane
Similarity search - Function
RNA-directed RNA polymerase L, filovirus / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V ...RNA-directed RNA polymerase L, filovirus / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / RNA-directed RNA polymerase L / Polymerase cofactor VP35
Similarity search - Component
Biological speciesMarburg virus - Musoke, Kenya, 1980 / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLi G / Du T / Wang J / Wu S / Ru H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371344 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the RNA-dependent RNA polymerase complexes from highly pathogenic Marburg and Ebola viruses.
Authors: Guobao Li / Tianjiao Du / Jiening Wang / Kaiyue Jie / Zhuolu Ren / Xiaokang Zhang / Long Zhang / Shan Wu / Heng Ru /
Abstract: The Ebola and the Marburg viruses belong to the Filoviridae family, a group of filamentous, single-stranded, negative-sensed RNA viruses. Upon infection, uncontrolled propagation of the Ebola and the ...The Ebola and the Marburg viruses belong to the Filoviridae family, a group of filamentous, single-stranded, negative-sensed RNA viruses. Upon infection, uncontrolled propagation of the Ebola and the Marburg viruses causes severe hemorrhagic fevers with high mortality rates. The replication and transcription of viral genomes are mediated by a polymerase complex consisting of two proteins: L and its cofactor VP35. However, the molecular mechanism of filovirus RNA synthesis remains understudied due to the lack of high-resolution structures of L and VP35 complexes from these viruses. Here, we present the cryo-EM structures of the polymerase complexes for the Marburg virus and the Ebola virus at 2.7 Å and 3.1 Å resolutions respectively. Despite the similar assembly and overall structures between these two viruses, we identify virus-specific L-VP35 interactions. Our data show that intergeneric exchange of VP35 would diminish these interactions and prevent the formation of a functional chimeric polymerase complex between L protein and heterologous VP35. Additionally, we identify a contracted conformation of the Ebola virus polymerase structure, revealing the structural dynamics of the polymerase during RNA synthesis. These insights enhance our understanding of filovirus RNA synthesis mechanisms and may facilitate the development of antiviral drugs targeting filovirus polymerase.
History
DepositionJul 10, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60755.png

Downloads & links

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Map

FileDownload / File: emd_60755.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 272.32 Å		0.85 Å/pix.
x 320 pix.
= 272.32 Å		0.85 Å/pix.
x 320 pix.
= 272.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.851 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.225
Minimum - Maximum-1.3614262 - 2.5134332
Average (Standard dev.)0.0005971793 (±0.052112877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60755_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_60755_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_60755_half_map_2.map
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Sample components

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Entire : Ternary complex of L-VP35 from Marburg virus

EntireName: Ternary complex of L-VP35 from Marburg virus
Components
  • Complex: Ternary complex of L-VP35 from Marburg virus
    • Protein or peptide: RNA-directed RNA polymerase L,Maltose/maltodextrin-binding periplasmic protein
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35
  • Ligand: ZINC ION

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Supramolecule #1: Ternary complex of L-VP35 from Marburg virus

SupramoleculeName: Ternary complex of L-VP35 from Marburg virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Marburg virus - Musoke, Kenya, 1980
Molecular weightTheoretical: 630 KDa

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Macromolecule #1: RNA-directed RNA polymerase L,Maltose/maltodextrin-binding peripl...

MacromoleculeName: RNA-directed RNA polymerase L,Maltose/maltodextrin-binding periplasmic protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 313.963656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQHPTQYPDA RLSSPIILDQ CDLLARSLGL YSHYSHNPKL RNCRIPHHIY RLRNSTALKT FLQNCSILTV PFHSIWDHIL TSIQYDAIN HVDDFKYLLP SELVKYANWD NEFLKAYLNK ILGLDHVFSA SARSQCEDFS PKENPYYWGM LLLVHLSQLA R RIKGQRGS ...String:
MQHPTQYPDA RLSSPIILDQ CDLLARSLGL YSHYSHNPKL RNCRIPHHIY RLRNSTALKT FLQNCSILTV PFHSIWDHIL TSIQYDAIN HVDDFKYLLP SELVKYANWD NEFLKAYLNK ILGLDHVFSA SARSQCEDFS PKENPYYWGM LLLVHLSQLA R RIKGQRGS LRSNWKFIGT DLELFGIADF VIFKVPVKTI IRNAVSLQAS KPGLRIWYRD QNLTPYLCDD EFIVSVASYE CF IMIKDVF IERYNTWEIC ARAWLEDSDG ADYPPLDVLG ELYNQGDQII AMYLEDGFKL IKHLEPLCVS CIQTHGIFTP RKY WFQSQM IKSYYDELHD LNLKLQISDN KAECAQNFIK TIVQAKLTPQ QYCELFSLQK HWGHPVLYND VALDKVKKHA QSTK ILKPK VMFETFCVFK FIVAKNHYHS QGSWYKTTHD LHLTPYLRQH IVSNSFPSQA EIYQHLWEWY FVEHEPLFST KIISD LSIF IKDRATAVNQ ECWDSVFDRS VLGYNPPVRF QSKRVPEQFL GQADFSLNQI LEFAEKLEYL APSYRNFSFS LKEKEL NIG RTFGKLPYRV RNVQTLAEAL LADGLAKAFP SNMMVVTERE QKEALLHQAS WHHNSASIGE NAIVRGASFV TDLEKYN LA FRYEFTRHFI DYCNRCYGVK NLFDWMHFLI PLCYMHVSDF YSPPHCVTED NRNNPPDCAN AYHYHLGGIE GLQQKLWT C ISCAQITLVE LKTKLKLKSS VMGDNQCITT LSLFPIDAPN DYQENEAELN AARVAVELAI TTGYSGIFLK PEETFVHSG FIYFGKKQYL NGVQLPQSLK TMARCGPLSD SIFDDLQGSL ASIGTSFERG TSETRHIFPS RWIASFHSML AINLLNQNHL GFPLGFNID ISCFKKPLTF SEKLIALITP QVLGGLSFLN PEKLFYRNIS DPLTSGLFQL KNALEFLEKE ELFYILISKK P GLADASDF VMNPLGLNVP GSKEIITFLR QTVRENITIT SQNRIINSLF HIGSDLEDQR VCEWLLSSNP VMSRFAADIF SR TPSGKRL QVLGYLEGTR TLLASRTISL TTEGTMLMKL RELTRNRWKS WFSYIDALDD DLSESLEKFT CTVDVANFLR AYS WSDVLK GKRLIGATLP CLLEQFEVKW INLSEDLREQ FNLSSDSKST INLLPYDCKE LRLEGSNDTE LNYVSCALDR KVVQ KHPSV NRLAWTIGNR APYIGSRTED KIGYPPLRVN CPSAALKEAI EMVSRLLWVT QGTADREKLL IPLLNSRVNL DYQTV LNFL PTHYSGNIVH RYNDQYGQHS FMANRMSNTS TRAIISTNTL GKYAGGGQAA IDSNIIFQNT INLGVAVLDI ALSLAK LSS ASNVTFRLML NKCCTRHVPS EYLYFDKPLD VDLNKYMDNE LVYDNDPLCS GIKGRLGRVS RSTLTLSLNV SDIGSYD FP TIAAWTLGET IVGSIFSDES SQSTDPISSG CTKTFVTHFL VYPVESIFYA FGANLIVESL SLSRIKSIKN LSDLTFLI S STIRNLSHRS LRILQSTFRH ELVLTRLAHH IPLISLMLGG SAGEKSSSDA VRLFLTASYQ NFINNFSCLM KKGQSSLPV WLYFPSEGQQ LKPILKILQR LSDLLSPDKI QKRKILADTC CPIGSFWVYP SKSTRTNHYY ASLNYWRDKA NKVKNTPFSH LINCSFPEF SSHTSSVSSN QQVTNSKYIV YPENITEINA RTRLINYGST ALQGMDTKMP LSEQNLVENC RPSEGIRFKD N QKITKHDQ RCEREESSPQ QMFPEDNMQT PAHIHSSSPF QILIKSLDAH EDFDASKIIL NSEINNLNLT EYTLNTKLLT TP TRTEILD TSPLQSSRYS STSRERSLLS REQASYLYVD CSNIPSISLD PGFRSMSDQN QVQMLINTYK RDLHACFDSN QFC RFTGVV SSMHYKLYDL LPPGKLKKAI CLAEGEGSGA RLLLKWKETD YLFFNTLATD SQQEAEILSG RVIPRMLYNI DRLS ALLES RRLILNNLTI QITDITNPLW LDSVIQYLPE DSDILTMDAE TTKDETREQL YKTIVNIWTR TSPNIPKISI IKVFL LDYE GTLFLMKNAI QYYGQVQLKK PYSSNAKNSE WYLCCGKRRI QRLQIDFSDQ VGIFLICKAM SRQRQAIPYW LKHIEK NYP ASLHEFFLTL GFPSLESSFC HRYTIPFSEG KALFHKVQSY VRQGKQHLHS LMLDYENNSP LLDLRNHFIC SLRGKIT KY YNDILKLNLV IKAVEKGKNW SQLVEILPNM HSVCIVHVDH ECSGCEKRLL LKLDFIRNTK IAEQKLLNRV IGYILFFP F GLFKSGSLRA SRENLYFQGS GWSHPQFEKG GGSGGGSGGS AWSHPQFEKG SASHHHHHHG TKTEEGKLVI WINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL MFNLQEPYFT WPLIAADGGY AFKYENGKYD I KDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NGPWAWSNID TSKVNYGVTV LPTFKGQPSK PF VGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYEEELAKDP RIAATMENAQ KGEIMPNIPQ MSA FWYAVR TAVINAASGR QTVDEALKDA QTGDYKDDDD K

UniProtKB: RNA-directed RNA polymerase L, Maltose/maltodextrin-binding periplasmic protein

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Macromolecule #2: Maltose/maltodextrin-binding periplasmic protein,Polymerase cofac...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Marburg virus - Musoke, Kenya, 1980
Molecular weightTheoretical: 79.880961 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH GTKTEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF ...String:
MGSSHHHHHH GTKTEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF TWPLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NG PWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYE EELAKD PRIAATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTGTDYDIPT TLEVLFQGPL GSMW DSSYM QQVSEGLMTG KVPIDQVFGA NPLEKLYKRR KPKGTVGLQC SPCLMSKATS TDDIIWDQLI VKRTLADLLI PINRQ ISDI QSTLSEVTTR VHEIERQLHE ITPVLKMGRT LEAISKGMSE MLAKYDHLVI STGRTTAPAA AFDAYLNEHG VPPPQP AIF KDLGVAQQAC SKGTMVKNAT TDAADKMSKV LELSEETFSK PNLSAKDLAL LLFTHLPGNN TPFHILAQVL SKIAYKS GK SGAFLDAFHQ ILSEGENAQA ALTRLSRTFD AFLGVVPPVI RVKNFQTVPR PCQKSLRAVP PNPTIDKGWV CVYSSEQG E TRALKI

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Polymerase cofactor VP35

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration1.2 mg/mL
BufferpH: 7.5 / Details: 25 mM HEPES, 500 mM NaCl, 1 mM TCEP, 6 mM MgCl2
VitrificationCryogen name: ETHANE
DetailsThis sample is monodisperse.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.52 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 319722
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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