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- EMDB-17351: Structure of hantaan orthohantavirus (HTNV) polymerase - Apo core -

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Basic information

Entry
Database: EMDB / ID: EMD-17351
TitleStructure of hantaan orthohantavirus (HTNV) polymerase - Apo core
Map data
Sample
  • Complex: RNA-dependent RNA polymerase of Hantaan orthohantavirus (HTNV).
    • Protein or peptide: RNA-directed RNA polymerase L
KeywordsRNA-dependent RNA polymerase / HTNV / Hantaan orthohantavirus / Bunyavirales / Hantaviridae. / VIRAL PROTEIN
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / endonuclease activity / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase, hantavirus / RNA-directed RNA polymerase, hantavirus, N-terminal / RNA dependent RNA polymerase / : / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / 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
Similarity search - Component
Biological speciesHantaan orthohantavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsKeown JR / Carrique L / Grimes JM
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R009945/1 United Kingdom
University of Oxford, Medical Sciences Internal Fund (MSIF)BDR00281 United Kingdom
CitationJournal: To Be Published
Title: Structure of hantaan orthohantavirus (HTNV) polymerase - Apo core
Authors: Keown JR / Carrique L / Grimes JM
History
DepositionMay 12, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17351.png

Downloads & links

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Map

FileDownload / File: emd_17351.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.932 Å
Density
Contour LevelBy AUTHOR: 0.356
Minimum - Maximum-2.3914275 - 3.3159232
Average (Standard dev.)-0.000084928135 (±0.07419058)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17351_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17351_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17351_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA-dependent RNA polymerase of Hantaan orthohantavirus (HTNV).

EntireName: RNA-dependent RNA polymerase of Hantaan orthohantavirus (HTNV).
Components
  • Complex: RNA-dependent RNA polymerase of Hantaan orthohantavirus (HTNV).
    • Protein or peptide: RNA-directed RNA polymerase L

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Supramolecule #1: RNA-dependent RNA polymerase of Hantaan orthohantavirus (HTNV).

SupramoleculeName: RNA-dependent RNA polymerase of Hantaan orthohantavirus (HTNV).
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hantaan orthohantavirus
Molecular weightTheoretical: 247 KDa

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Macromolecule #1: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Hantaan orthohantavirus
Molecular weightTheoretical: 251.806016 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK HHHHHHHHEN LYFQGMDKYR EIHNKLKEFS PGTLTAVECI DYLDRLYAVR HDIVDQMIK HDWSDNKDSE EAIGKVLLFA GVPSNIITAL EKKIIPNHPT GKSLKAFFKM TPANYKISGT TIEFVEVTVT A DVDKGIRE ...String:
MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK HHHHHHHHEN LYFQGMDKYR EIHNKLKEFS PGTLTAVECI DYLDRLYAVR HDIVDQMIK HDWSDNKDSE EAIGKVLLFA GVPSNIITAL EKKIIPNHPT GKSLKAFFKM TPANYKISGT TIEFVEVTVT A DVDKGIRE KKLKYEAGLT YIEQELHKFF LKGEIPQPYK ITFNVVAVRT DGSNITTQWP SRRNDGVVQY MRLVQAEISY VR EHLIKTE ERAALEAMFN LKFNISTHKS QPYYIPDYKG MEPIGANIED LVDYSKDWLS RARNFSFFEV KGTAVFECFN SNE ANHCQR YPMSRKPRNF LLIQCSLITS YKPATTLSDQ IDSRRACSYI LNLIPDTPAS YLIHDMAYRY INLTREDMIN YYAP RIQFK QTQNVREPGT FKLTSSMLRA ESKAMLDLLN NHKSGEKHGA QIESLNIASH IVQSESVSLI TKILSDLELN ITEPS TQEY STTKHTYVDT VLDKFFQNET QKYLIDVLKK TTAWHIGHLI RDITESLIAH SGLKRSKYWS LHSYNNGNVI LFILPS KSL EVAGSFIRFI TVFRIGPGLV DKDNLDTILI DGDSQWGVSK VMSIDLNRLL ALNIAFEKAL IATATWFQYY TEDQGQF PL QYAIRSVFAN HFLLAICQKM KLCAIFDNLR YLIPAVTSLY SGFPSLIEKL FERPFKSSLE VYIYYNIKSL LVALAQNN K ARFYSKVKLL GLTVDQSTVG ASGVYPSFMS RIVYKHYRSL ISEVTTCFFL FEKGLHGNMN EEAKIHLETV EWALKFREK EEKYGESLVE NGYMMWELRA NAELAEQQLY CQDAIELAAI ELNKVLATKS SVVANSILSK NWEEPYFSQT RNISLKGMSG QVQEDGHLS SSVTIIEAIR YLSNSRHNPS LLKLYEETRE QKAMARIVRK YQRTEADRGF FITTLPTRCR LEIIEDYYDA I AKNISEEY ISYGGEKKIL AIQGALEKAL RWASGESFIE LSNHKFIRMK RKLMYVSADA TKWSPGDNSA KFRRFTSMLH NG LPNNKLK NCVIDALKQV YKTDFFMSRK LRNYIDSMES LDPHIKQFLD FFPDGHHGEV KGNWLQGNLN KCSSLFGVAM SLL FKQVWT NLFPELDCFF EFAHHSDDAL FIYGYLEPVD DGTDWFLFVS QQIQAGHLHW FSVNTEMWKS MFNLHEHILL LGSI KISPK KTTVSPTNAE FLSTFFEGCA VSIPFVKILL GSLSDLPGLG YFDDLAAAQS RCVKALDLGA SPQVAQLAVA LCTSK VERL YGTAPGMVNH PAAYLQVKHT DTPIPLGGNG AMSIMELATA GIGMSDKNLL KRALLGYSHK RQKSMLYILG LFKFLM KLS DETFQHERLG QFSFIGKVQW KIFTPKSEFE FADMYTSKFL ELWSSQHVTY DYIIPKGRDN LLIYLVRKLN DPSIVTA MT MQSPLQLRFR MQAKQHMKVC RLDGEWVTFR EVLAAANSFA ENYSATSQDM DLFQTLTSCT FSKEYAWKDF LNGIHCDV I PTKQVQRAKV ARTFTVREKD QIIQNSIPAV IGYKFAVTVE EMSDVLDTAK FPDSLSVDLK TMKDGVYREL GLDISLPDV MKRIAPMLYK SSKSRVVIVQ GNVEGTAEAI CRYWLKSMSL VKTIRVKPHK EVLQAVSIFN RKEDIGQQKD LAALKLCIEV WRWCKANSA PYRDWFQALW FEDKTFSEWL DRFCRVGVPP IDPEIQCAAL MIADIKGDYS VLQLQANRRA YSGKQYDAYC V QTYNEVTK LYEGDLRVTF NFGLDCARLE IFWDKKAYIL ETSITQKHVL KIMMDEVSKE LIKCGMRFNT EQVQGVRHMV LF KTESGFE WGKPNIPCIV YKNCVLRTSL RTTQAINHKF MITIKDDGLR AIAQHDEDSP RFLLAHAFHT IRDIRYQAVD AVS NVWFIH KGVKLYLNPI ISSGLLENFM KNLPAAIPPA AYSLIMNRAK ISVDLFMFND LLKLINPRNT LDLSGLETTG DEFS TVSSM SSRLWSEEMS LVDDDEELDD EFTIDLQDVD FENIDIEADI EHFLQDESSY TGDLLISTEE TESKKMRGIV KILEP VRLI KSWVSRGLSI EKVYSPVNII LMSRYISKTF NLSTKQVSLL DPYDLTELES IVRGWGECVI DQFESLDREA QNMVVN KGI CPEDVIPDSL FSFRHTMVLL RRLFPQDSIS SFY

UniProtKB: RNA-directed RNA polymerase L

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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

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
500.0 mMNaClSodium chloridesodium chloride
1.0 mMDTTdithiothreitol
5.0 %GlycerolGlycerol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Alphafold2 model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final 3D classificationNumber classes: 8 / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 500000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-8p1j:
Structure of hantaan orthohantavirus (HTNV) polymerase - Apo core

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