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- PDB-7x6v: lymphocytic choriomeningitis virus polymerase- Matrix Z Protein C... -

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Basic information

Entry
Database: PDB / ID: 7x6v
Titlelymphocytic choriomeningitis virus polymerase- Matrix Z Protein Complex (LCMV L-Z Complex)
Components
  • RING finger protein Z
  • RNA-directed RNA polymerase L
KeywordsMETAL BINDING PROTEIN/TRANSFERASE / L protein / RING finger protein / METAL BINDING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


negative stranded viral RNA replication / cap snatching / viral budding via host ESCRT complex / viral budding from plasma membrane / virion component / host cell / Hydrolases; Acting on ester bonds / host cell cytoplasm / hydrolase activity / host cell perinuclear region of cytoplasm ...negative stranded viral RNA replication / cap snatching / viral budding via host ESCRT complex / viral budding from plasma membrane / virion component / host cell / Hydrolases; Acting on ester bonds / host cell cytoplasm / hydrolase activity / host cell perinuclear region of cytoplasm / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / host cell plasma membrane / RNA binding / zinc ion binding / metal ion binding / membrane
Similarity search - Function
RING finger protein Z, zinc finger / RING finger protein Z, arenaviridae / Protein Z, RING-type zinc finger superfamily / P-11 zinc finger / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / : / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
: / RNA-directed RNA polymerase L / RING finger protein Z
Similarity search - Component
Biological speciesLymphocytic choriomeningitis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu, L. / Lou, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Protein Cell / Year: 2023
Title: Structure basis for allosteric regulation of lymphocytic choriomeningitis virus polymerase function by Z matrix protein.
Authors: Lu Liu / Panpan Wang / Aijun Liu / Leike Zhang / Liming Yan / Yu Guo / Gengfu Xiao / Zihe Rao / Zhiyong Lou /
History
DepositionMar 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
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Revision 1.1Sep 27, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RING finger protein Z
A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,2795
Polymers265,0932
Non-polymers1863
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein RING finger protein Z


Mass: 10198.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis virus (strain Armstrong)
Strain: Armstrong / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P18541
#2: Protein RNA-directed RNA polymerase L


Mass: 254894.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis virus (strain Armstrong)
Strain: Armstrong / Production host: unidentified baculovirus / References: UniProt: A0A218M2D5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / 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

Component
IDNameTypeEntity IDParent-IDSource
1The complex of LCMV polymerase with matrix protein ZCOMPLEX#1-#20RECOMBINANT
2matrix protein ZCOMPLEX#11RECOMBINANT
3LCMV polymerase L proteinCOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Lymphocytic choriomeningitis virus (strain Armstrong)11624
33Lymphocytic choriomeningitis virus (strain Armstrong)11624
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli BL21 (bacteria)511693
33unidentified baculovirus10469
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 1.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98004 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00911177
ELECTRON MICROSCOPYf_angle_d0.93215133
ELECTRON MICROSCOPYf_dihedral_angle_d22.5211520
ELECTRON MICROSCOPYf_chiral_restr0.0511721
ELECTRON MICROSCOPYf_plane_restr0.0051953

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