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- PDB-9ip2: Cryo-EM structure of the RNA-dependent RNA polymerase complex fro... -

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Basic information

Entry
Database: PDB / ID: 9ip2
TitleCryo-EM structure of the RNA-dependent RNA polymerase complex from Marburg virus
Components
  • Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35
  • RNA-directed RNA polymerase L,Maltose/maltodextrin-binding periplasmic protein
KeywordsVIRAL PROTEIN / RNA-dependent RNA polymerase complex
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 / carbohydrate transmembrane transporter activity / maltose binding / maltose transport ...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 / 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 / cell chemotaxis / outer membrane-bounded periplasmic space / viral nucleocapsid / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / periplasmic space / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase 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. / 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
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLi, G. / Du, T. / Wang, J. / Wu, S. / Ru, H.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L,Maltose/maltodextrin-binding periplasmic protein
B: Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35
C: Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35
D: Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35
E: Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)633,5536
Polymers633,4885
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein RNA-directed RNA polymerase L,Maltose/maltodextrin-binding periplasmic protein / Protein L / Large structural protein / Replicase / Transcriptase / MMBP / Maltodextrin-binding ...Protein L / Large structural protein / Replicase / Transcriptase / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 313963.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marburg virus - Musoke, Kenya, 1980, (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: malE, b4034, JW3994 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P31352, UniProt: P0AEX9, RNA-directed RNA polymerase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, GDP polyribonucleotidyltransferase, NNS virus cap methyltransferase
#2: Protein
Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Marburg VP35 / mVP35


Mass: 79880.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Marburg virus - Musoke, Kenya, 1980
Gene: malE, b4034, JW3994, VP35 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0AEX9, UniProt: P35259
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of L-VP35 from Marburg virus / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.63 MDa / Experimental value: NO
Source (natural)Organism: Marburg virus - Musoke, Kenya, 1980
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5 / Details: 25 mM HEPES, 500 mM NaCl, 1 mM TCEP, 6 mM MgCl2
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample is monodisperse.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 52.52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 319722 / Symmetry type: POINT
RefinementResolution: 2.7→306.36 Å / SU ML: 0.25 / σ(F): 0.28 / Phase error: 38.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3006 2040 7 %
Rwork0.2944 --
obs0.2944 3059311 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01313923
ELECTRON MICROSCOPYf_angle_d1.46318870
ELECTRON MICROSCOPYf_dihedral_angle_d15.3271833
ELECTRON MICROSCOPYf_chiral_restr0.0772106
ELECTRON MICROSCOPYf_plane_restr0.0092400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.58021200.5904204777ELECTRON MICROSCOPY100
2.76-2.830.5341680.5436203498ELECTRON MICROSCOPY100
2.83-2.910.5091200.5338203626ELECTRON MICROSCOPY100
2.91-2.990.48631440.5316203783ELECTRON MICROSCOPY100
2.99-3.090.50441440.5031204245ELECTRON MICROSCOPY100
3.09-3.20.4971320.4675203522ELECTRON MICROSCOPY100
3.2-3.330.37571080.4265203969ELECTRON MICROSCOPY100
3.33-3.480.38421440.3746203789ELECTRON MICROSCOPY100
3.48-3.660.37711320.3292203357ELECTRON MICROSCOPY100
3.66-3.890.2821440.278203967ELECTRON MICROSCOPY100
3.89-4.190.27521440.2289204153ELECTRON MICROSCOPY100
4.2-4.620.22351320.1912203839ELECTRON MICROSCOPY100
4.62-5.280.17971320.182204011ELECTRON MICROSCOPY100
5.29-6.660.22461200.2085203701ELECTRON MICROSCOPY100
6.66-306.360.16491560.188203034ELECTRON MICROSCOPY100

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