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- EMDB-60756: Cryo-EM structure of the RNA-dependent RNA polymerase complex in ... -

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Entry
Database: EMDB / ID: EMD-60756
TitleCryo-EM structure of the RNA-dependent RNA polymerase complex in a compact conformation from Ebola virus
Map data
Sample
  • Complex: Ternary complex of L-VP35 core region from Ebola virus
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,RNA-directed RNA polymerase L
    • 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


RNA polymerase activity / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative stranded viral RNA transcription / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / NNS virus cap methyltransferase / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / GDP polyribonucleotidyltransferase ...RNA polymerase activity / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative stranded viral RNA transcription / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / NNS virus cap methyltransferase / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / GDP polyribonucleotidyltransferase / symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of protein sumoylation / negative stranded viral RNA replication / detection of maltose stimulus / maltose transport complex / carbohydrate transport / viral transcription / molecular sequestering activity / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / viral genome replication / cell chemotaxis / virion component / outer membrane-bounded periplasmic space / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral nucleocapsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / periplasmic space / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / negative regulation of gene expression / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / DNA damage response / RNA binding / 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. / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. ...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. / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Polymerase cofactor VP35 / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesEbola virus - Eckron (Zaire, 1976)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_60756.png

Downloads & links

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Map

FileDownload / File: emd_60756.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-1.9661987 - 2.8379185
Average (Standard dev.)0.0006904532 (±0.078447685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60756_msk_1.map
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Half map: #2

Fileemd_60756_half_map_1.map
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Half map: #1

Fileemd_60756_half_map_2.map
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Sample components

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Entire : Ternary complex of L-VP35 core region from Ebola virus

EntireName: Ternary complex of L-VP35 core region from Ebola virus
Components
  • Complex: Ternary complex of L-VP35 core region from Ebola virus
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,RNA-directed RNA polymerase L
    • 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 core region from Ebola virus

SupramoleculeName: Ternary complex of L-VP35 core region from Ebola virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Ebola virus - Eckron (Zaire, 1976)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,RNA-directed RNA...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,RNA-directed RNA polymerase L
type: protein_or_peptide / ID: 1
Details: Sequence reference for Ebola virus - Eckron (Zaire, 1976) (12900) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID Q05318.
Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Ebola virus - Eckron (Zaire, 1976)
Molecular weightTheoretical: 207.335219 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSGWSHPQF EKGGGSGGGS GGSAWSHPQF EKGSASHHHH HHGTKTEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL I YNKDLLPN ...String:
MGSGWSHPQF EKGGGSGGGS GGSAWSHPQF EKGSASHHHH HHGTKTEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL I YNKDLLPN PPKTWEEIPA LDKELKAKGK SALMFNLQEP YFTWPLIAAD GGYAFKYENG KYDIKDVGVD NAGAKAGLTF LV DLIKNKH MNADTDYSIA EAAFNKGETA MTINGPWAWS NIDTSKVNYG VTVLPTFKGQ PSKPFVGVLS AGINAASPNK ELA KEFLEN YLLTDEGLEA VNKDKPLGAV ALKSYEEELA KDPRIAATME NAQKGEIMPN IPQMSAFWYA VRTAVINAAS GRQT VDEAL KDAQTGTDYD IPTTLEVLFQ GPGSMATQHT QYPDARLSSP IVLDQCDLVT RACGLYSSYS LNPQLRNCKL PKHIY RLKY DVTVTKFLSD VPVATLPIDF IVPVLLKALS GNGFCPVEPR CQQFLDEIIK YTMQDALFLK YYLKNVGAQE DCVDEH FQE KILSSIQGNE FLHQMFFWYD LAILTRRGRL NRGNSRSTWF VHDDLIDILG YGDYVFWKIP ISMLPLNTQG IPHAAMD WY QASVFKEAVQ GHTHIVSVST ADVLIMCKDL ITCRFNTTLI SKIAEIEDPV CSDYPNFKIV SMLYQSGDYL LSILGSDG Y KIIKFLEPLC LAKIQLCSKY TERKGRFLTQ MHLAVNHTLE EITEMRALKP SQAQKIREFH RTLIRLEMTP QQLCELFSI QKHWGHPVLH SETAIQKVKK HATVLKALRP IVIFETYCVF KYSIAKHYFD SQGSWYSVTS DRNLTPGLNS YIKRNQFPPL PMIKELLWE FYHLDHPPLF STKIISDLSI FIKDRATAVE RTCWDAVFEP NVLGYNPPHK FSTKRVPEQF LEQENFSIEN V LSYAQKLE YLLPQYRNFS FSLKEKELNV GRTFGKLPYP TRNVQTLCEA LLADGLAKAF PSNMMVVTER EQKESLLHQA SW HHTSDDF GEHATVRGSS FVTDLEKYNL AFRYEFTAPF IEYCNRCYGV KNVFNWMHYT IPQCYMHVSD YYNPPHNLTL ENR DNPPEG PSSYRGHMGG IEGLQQKLWT SISCAQISLV EIKTGFKLRS AVMGDNQCIT VLSVFPLETD ADEQEQSAED NAAR VAASL AKVTSACGIF LKPDETFVHS GFIYFGKKQY LNGVQLPQSL KTATRMAPLS DAIFDDLQGT LASIGTAFER SISET RHIF PCRITAAFHT FFSVRILQYH HLGFNKGFDL GQLTLGKPLD FGTISLALAV PQVLGGLSFL NPEKCFYRNL GDPVTS GLF QLKTYLRMIE MDDLFLPLIA KNPGNCTAID FVLNPSGLNV PGSQDLTSFL RQIVRRTITL SAKNKLINTL FHASADF ED EMVCKWLLSS TPVMSRFAAD IFSRTPSGKR LQILGYLEGT RTLLASKIIN NNTETPVLDR LRKITLQRWS LWFSYLDH C DNILAEALTQ ITCTVDLAQI LREYSWAHIL EGRPLIGATL PCMIEQFKVF WLKPYEQCPQ CSNAKQPGGK PFVSVAVKK HIVSAWPNAS RISWTIGDGI PYIGSRTEDK IGQPAIKPKC PSAALREAIE LASRLTWVTQ GSSNSDLLIK PFLEARVNLS VQEILQMTP SHYSGNIVHR YNDQYSPHSF MANRMSNSAT RLIVSTNTLG EFSGGGQSAR DSNIIFQNVI NYAVALFDIK F RNTEATDI QYNRAHLHLT KCCTREVPAQ YLTYTSTLDL DLTRYRENEL IYDSNPLKGG LNCNISFDNP FSRDYKDDDD K

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

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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
Details: Sequence reference for Ebola virus - Eckron (Zaire, 1976) (12900) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID Q05127.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Eckron (Zaire, 1976)
Molecular weightTheoretical: 72.190336 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 TENLYFQGGS NHSF EEVVQ TLASLATVVQ QQTIASESLE QRITSLENGL KPVYDMAKTI SSLNRVCAEM VAKYDLLVMT TGRATATAAA TEAYW AEHG QPPPGPSLYE ESAIRGKIES RDETVPQSVR EAFNNLNSTT SLTEENFGKP DISAKDLRNI MYDHLPGFGT AFHQLV QVI CKLGKDSNSL DIIHAEFQAS LAEGDSPQCA LIQITKRVPI FQDAAPPVIH IRSRGDIPRA CQKSLRPVPP SPKIDRG WV CVFQLQDGKT LGLKI

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, 300 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: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77587
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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