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- EMDB-20753: Structure of Rabies SAD-B19 L-P complex from cryo-EM -

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Basic information

Entry
Database: EMDB / ID: EMD-20753
TitleStructure of Rabies SAD-B19 L-P complex from cryo-EM
Map dataFinal B-factor sharpened, clipped, full EM map into which the structure was fit
Sample
  • Complex: Rabies lyssavirus strain SAD-B19 L-P complex
    • Protein or peptide: Large structural protein
    • Protein or peptide: Phosphoprotein,Phosphoprotein
  • Ligand: ZINC ION
KeywordsPolymerase / Phosphoprotein / Complex / VIRAL PROTEIN
Function / homology
Function and homology information


NNS virus cap methyltransferase / symbiont-mediated suppression of host transcription / GDP polyribonucleotidyltransferase / microtubule-dependent intracellular transport of viral material towards nucleus / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component ...NNS virus cap methyltransferase / symbiont-mediated suppression of host transcription / GDP polyribonucleotidyltransferase / microtubule-dependent intracellular transport of viral material towards nucleus / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / virus-mediated perturbation of host defense response / host cell nucleus / ATP binding
Similarity search - Function
: / Virus-capping methyltransferase, C-terminal / RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / : / Phosphoprotein / Phosphoprotein, C-terminal / Phosphoprotein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus ...: / Virus-capping methyltransferase, C-terminal / RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / : / Phosphoprotein / Phosphoprotein, C-terminal / Phosphoprotein / 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.
Similarity search - Domain/homology
Phosphoprotein / Large structural protein
Similarity search - Component
Biological speciesRabies virus (strain SAD B19)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHorwitz JA / Harrison SC
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of a rabies virus polymerase complex from electron cryo-microscopy.
Authors: Joshua A Horwitz / Simon Jenni / Stephen C Harrison / Sean P J Whelan /
Abstract: Nonsegmented negative-stranded (NNS) RNA viruses, among them the virus that causes rabies (RABV), include many deadly human pathogens. The large polymerase (L) proteins of NNS RNA viruses carry all ...Nonsegmented negative-stranded (NNS) RNA viruses, among them the virus that causes rabies (RABV), include many deadly human pathogens. The large polymerase (L) proteins of NNS RNA viruses carry all of the enzymatic functions required for viral messenger RNA (mRNA) transcription and replication: RNA polymerization, mRNA capping, and cap methylation. We describe here a complete structure of RABV L bound with its phosphoprotein cofactor (P), determined by electron cryo-microscopy at 3.3 Å resolution. The complex closely resembles the vesicular stomatitis virus (VSV) L-P, the one other known full-length NNS-RNA L-protein structure, with key local differences (e.g., in L-P interactions). Like the VSV L-P structure, the RABV complex analyzed here represents a preinitiation conformation. Comparison with the likely elongation state, seen in two structures of pneumovirus L-P complexes, suggests differences between priming/initiation and elongation complexes. Analysis of internal cavities within RABV L suggests distinct template and product entry and exit pathways during transcription and replication.
History
DepositionSep 20, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseFeb 5, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ueb
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20753.png

Downloads & links

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Map

FileDownload / File: emd_20753.map.gz / Format: CCP4 / Size: 6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal B-factor sharpened, clipped, full EM map into which the structure was fit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 116 pix.
= 143.144 Å		1.23 Å/pix.
x 116 pix.
= 143.144 Å		1.23 Å/pix.
x 116 pix.
= 143.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.234 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0 / Movie #1: 5
Minimum - Maximum-12.308636 - 23.361754999999999
Average (Standard dev.)0.014836848 (±1.8893837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions116116116
Spacing116116116
CellA=B=C: 143.144 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2341.2341.234
M x/y/z116116116
origin x/y/z0.0000.0000.000
length x/y/z143.144143.144143.144
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS116116116
D min/max/mean-12.30923.3620.015

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Supplemental data

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Additional map: Final unsharpened, unclipped EM map

Fileemd_20753_additional.map
AnnotationFinal unsharpened, unclipped EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map #1

Fileemd_20753_half_map_1.map
Annotationhalf map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map #2

Fileemd_20753_half_map_2.map
Annotationhalf map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rabies lyssavirus strain SAD-B19 L-P complex

EntireName: Rabies lyssavirus strain SAD-B19 L-P complex
Components
  • Complex: Rabies lyssavirus strain SAD-B19 L-P complex
    • Protein or peptide: Large structural protein
    • Protein or peptide: Phosphoprotein,Phosphoprotein
  • Ligand: ZINC ION

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Supramolecule #1: Rabies lyssavirus strain SAD-B19 L-P complex

SupramoleculeName: Rabies lyssavirus strain SAD-B19 L-P complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Purified L-P(1-91) complexes from baculovirus co-expression in insect cells
Source (natural)Organism: Rabies virus (strain SAD B19)

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Macromolecule #1: Large structural protein

MacromoleculeName: Large structural protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Rabies virus (strain SAD B19) / Strain: SAD B19
Molecular weightTheoretical: 243.274344 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLDPGEVYDD PIDPIELEAE PRGTPIVPNI LRNSDYNLNS PLIEDPARLM LEWLKTGNRP YRMTLTDNCS RSFRVLKDYF KKVDLGSLK VGGMAAQSMI SLWLYGAHSE SNRSRRCITD LAHFYSKSSP IEKLLNLTLG NRGLRIPPEG VLSCLERVDY D NAFGRYLA ...String:
MLDPGEVYDD PIDPIELEAE PRGTPIVPNI LRNSDYNLNS PLIEDPARLM LEWLKTGNRP YRMTLTDNCS RSFRVLKDYF KKVDLGSLK VGGMAAQSMI SLWLYGAHSE SNRSRRCITD LAHFYSKSSP IEKLLNLTLG NRGLRIPPEG VLSCLERVDY D NAFGRYLA NTYSSYLFFH VITLYMNALD WDEEKTILAL WKDLTSVDIG KDLVKFKDQI WGLLIVTKDF VYSQSSNCLF DR NYTLMLK DLFLSRFNSL MVLLSPPEPR YSDDLISQLC QLYIAGDQVL SMCGNSGYEV IKILEPYVVN SLVQRAEKFR PLI HSLGDF PVFIKDKVSQ LEETFGPCAR RFFRALDQFD NIHDLVFVFG CYRHWGHPYI DYRKGLSKLY DQVHLKKMID KSYQ ECLAS DLARRILRWG FDKYSKWYLD SRFLARDHPL TPYIKTQTWP PKHIVDLVGD TWHKLPITQI FEIPESMDPS EILDD KSHS FTRTRLASWL SENRGGPVPS EKVIITALSK PPVNPREFLR SIDLGGLPDE DLIIGLKPKE RELKIEGRFF ALMSWN LRL YFVITEKLLA NYILPLFDAL TMTDNLNKVF KKLIDRVTGQ GLLDYSRVTY AFHLDYEKWN NHQRLESTED VFSVLDQ VF GLKRVFSRTH EFFQKAWIYY SDRSDLIGLR EDQIYCLDAS NGPTCWNGQD GGLEGLRQKG WSLVSLLMID RESQIRNT R TKILAQGDNQ VLCPTYMLSP GLSQEGLLYE LERISRNALS IYRAVEEGAS KLGLIIKKEE TMCSYDFLIY GKTPLFRGN ILVPESKRWA RVSCVSNDQI VNLANIMSTV STNALTVAQH SQSLIKPMRD FLLMSVQAVF HYLLFSPILK GRVYKILSAE GESFLLAMS RIIYLDPSLG GISGMSLGRF HIRQFSDPVS EGLSFWREIW LSSQESWIHA LCQEAGNPDL GERTLESFTR L LEDPTTLN IRGGASPTIL LKDAIRKALY DEVDKVENSE FREAILLSKT HRDNFILFLI SVEPLFPRFL SELFSSSFLG IP ESIIGLI QNSRTIRRQF RKSLSKTLEE SFYNSEIHGI SRMTQTPQRV GGVWPCSSER ADLLREISWG RKVVGTTVPH PSE MLGLLP KSSISCTCGA TGGGNPRVSV SVLPSFDQSF FSRGPLKGYL GSSTSMSTQL FHAWEKVTNV HVVKRALSLK ESIN WFITR DSNLAQALIR NIMSLTGPDF PLEEAPVFKR TGSALHRFKS ARYSEGGYSS VCPNLLSHIS VSTDTMSDLT QDGKN YDFM FQPLMLYAQT WTSELVQRDT RLRDSTFHWH LRCNRCVRPI DDVTLETSQI FEFPDVSKRI SRMVSGAVPH FQRLPD IRL RPGDFESLSG REKSHHIGSA QGLLYSILVA IHDSGYNDGT IFPVNIYGKV SPRDYLRGLA RGVLIGSSIC FLTRMTN IN INRPLELVSG VISYILLRLD NHPSLYIMLR EPSLRGEIFS IPQKIPAAYP TTMKEGNRSI LCYLQHVLRY EREIITAS P ENDWLWIFSD FRSAKMTYLS LITYQSHLLL QRVERNLSKS MRDNLRQLSS LMRQVLGGHG EDTLESDDNI QRLLKDSLR RTRWVDQEVR HAARTMTGDY SPNKKVSRKV GCSEWVCSAQ QVAVSTSANP APVSELDIRA LSKRFQNPLI SGLRVVQWAT GAHYKLKPI LDDLNVFPSL CLVVGDGSGG ISRAVLNMFP DAKLVFNSLL EVNDLMASGT HPLPPSAIMR GGNDIVSRVI D LDSIWEKP SDLRNLATWK YFQSVQKQVN MSYDLIICDA EVTDIASINR ITLLMSDFAL SIDGPLYLVF KTYGTMLVNP NY KAIQHLS RAFPSVTGFI TQVTSSFSSE LYLRFSKRGK FFRDAEYLTS STLREMSLVL FNCSSPKSEM QRARSLNYQD LVR GFPEEI ISNPYNEMII TLIDSDVESF LVHKMVDDLE LQRGTLSKVA IIIAIMIVFS NRVFNVSKPL TDPSFYPPSD PKIL RHFNI CCSTMMYLST ALGDVPSFAR LHDLYNRPIT YYFRKQVIRG NVYLSWSWSN DTSVFKRVAC NSSLSLSSHW IRLIY KIVK TTRLVGSIKD LSREVERHLH RYNRWITLED IRSRSSLLDY SCL

UniProtKB: Large structural protein

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Macromolecule #2: Phosphoprotein,Phosphoprotein

MacromoleculeName: Phosphoprotein,Phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabies virus (strain SAD B19) / Strain: SAD B19
Molecular weightTheoretical: 4.623038 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)EDMGR LHLDDGKSPN HGEIAKVGEG KYREDFQMDE GE

UniProtKB: Phosphoprotein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / 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

Concentration0.3 mg/mL
BufferpH: 8.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: cisTEM was used for the final reconstruction and FSC curve/resolution analysis.
Number images used: 44500
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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