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- PDB-5a22: Structure of the L protein of vesicular stomatitis virus from ele... -

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Basic information

Entry
Database: PDB / ID: 5a22
TitleStructure of the L protein of vesicular stomatitis virus from electron cryomicroscopy
ComponentsVESICULAR STOMATITIS VIRUS L POLYMERASE
KeywordsTRANSFERASE / RNA-DEPENDENT RNA POLYMERASE / RNA CAPPING / CRYOEM SINGLE- PARTICLE ANALYSIS
Function / homology
Function and homology information


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity ...NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / ATP binding / metal ion binding
Similarity search - Function
: / Virus-capping methyltransferase, C-terminal / RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V ...: / Virus-capping methyltransferase, C-terminal / RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesVESICULAR STOMATITIS VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiang, B. / Li, Z. / Jenni, S. / Rameh, A.A. / Morin, B.M. / Grant, T. / Grigorieff, N. / Harrison, S.C. / Whelan, S.P.J.
CitationJournal: Cell / Year: 2015
Title: Structure of the L Protein of Vesicular Stomatitis Virus from Electron Cryomicroscopy.
Authors: Bo Liang / Zongli Li / Simon Jenni / Amal A Rahmeh / Benjamin M Morin / Timothy Grant / Nikolaus Grigorieff / Stephen C Harrison / Sean P J Whelan /
Abstract: The large (L) proteins of non-segmented, negative-strand RNA viruses, a group that includes Ebola and rabies viruses, catalyze RNA-dependent RNA polymerization with viral ribonucleoprotein as ...The large (L) proteins of non-segmented, negative-strand RNA viruses, a group that includes Ebola and rabies viruses, catalyze RNA-dependent RNA polymerization with viral ribonucleoprotein as template, a non-canonical sequence of capping and methylation reactions, and polyadenylation of viral messages. We have determined by electron cryomicroscopy the structure of the vesicular stomatitis virus (VSV) L protein. The density map, at a resolution of 3.8 Å, has led to an atomic model for nearly all of the 2109-residue polypeptide chain, which comprises three enzymatic domains (RNA-dependent RNA polymerase [RdRp], polyribonucleotidyl transferase [PRNTase], and methyltransferase) and two structural domains. The RdRp resembles the corresponding enzymatic regions of dsRNA virus polymerases and influenza virus polymerase. A loop from the PRNTase (capping) domain projects into the catalytic site of the RdRp, where it appears to have the role of a priming loop and to couple product elongation to large-scale conformational changes in L.
History
DepositionMay 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id / _em_software.name
Revision 1.2Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-6337
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Assembly

Deposited unit
A: VESICULAR STOMATITIS VIRUS L POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,4453
Polymers241,3141
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein VESICULAR STOMATITIS VIRUS L POLYMERASE


Mass: 241313.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VESICULAR STOMATITIS VIRUS / Strain: INDIANA / Variant: SAN JUAN ISOLATE / Plasmid: PFASTBAC DUAL (INVITROGEN) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P03523, DNA-directed RNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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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: VESICULAR STOMATITIS VIRUS RNA- DEPENDENT RNA POLYMERASE (L) BOUND TO PHOSPHOPROTEIN P FRAGMENT
Type: COMPLEX
Buffer solutionName: 25 MM HEPES, 250 MM NACL, 6 MM MGSO4, 0.5 MM TCEP / pH: 7.4 / Details: 25 MM HEPES, 250 MM NACL, 6 MM MGSO4, 0.5 MM TCEP
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Aug 1, 2014 / Details: GOOD MICROGRAPHS WERE SELECTED FOR DIGITISATION
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 29000 X / Calibrated magnification: 40410 X / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm / Cs: 2 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 1272
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1EMAN23D reconstruction
2FREALIGN3D reconstruction
3IMAGIC3D reconstruction
CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 3.8 Å / Num. of particles: 74940 / Nominal pixel size: 1.72 Å / Actual pixel size: 1.24 Å
Details: FREALIGN WAS USED FOR REFINEMENT AND THREE- DIMENSIONAL CLASSIFICATION. SEGMENTS A1159-A1171, A1210-A1226, A1308-1334, A1387-A1395, A1512-A1516, A1534-A1541 ARE IN POOR DENSITY, AND THE ...Details: FREALIGN WAS USED FOR REFINEMENT AND THREE- DIMENSIONAL CLASSIFICATION. SEGMENTS A1159-A1171, A1210-A1226, A1308-1334, A1387-A1395, A1512-A1516, A1534-A1541 ARE IN POOR DENSITY, AND THE CHAIN TRACE IN THOSE REGIONS IS APPROXIMATE. STEREOCHEMISTRY OF ZN A3000, A3001 COORDINATION IS POOR. DEPOSITED STRUCTURE FACTORS USED FOR REFINEMENT OF THIS ENTRY ARE FROM SOLVENT FLATTENED EM MAP EMD CODE 6337 AFTER PLACING THE DENSITY INTO A CELL WITH DIMESIONS 112.000, 143.000, 106.000 AND ANGLES 90.00,90.00,90.00. APPLY THE FOLLOWING TRANSFORMATION MATRIX TO THE COORDINATES IN ORDER TO PLACE THE MODEL INTO THE DENSITY CALCULATED FROM THE DEPOSITED STRUCTURE FACTORS: MODEL2SF 1 -0.492787 0.222962 -0.841098 139.886 MODEL2SF 1 -0.456450 -0.889187 0.031721 169.772 MODEL2SF 1 -0.740818 0.399552 0.539950 33.800
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: Maximum likelihood / Details: METHOD--PHENIX.REFINE
RefinementHighest resolution: 3.8 Å
Refinement stepCycle: LAST / Highest resolution: 3.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16075 0 2 0 16077

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