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- EMDB-45805: Infectious bronchitis virus core polymerase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45805
TitleInfectious bronchitis virus core polymerase complex
Map data
Sample
  • Complex: Core polymerase complex of the infectious bronchitis virus composed of nsp12, nsp8, nsp7, and an dsRNA substrate
    • Protein or peptide: RNA-directed RNA polymerase nsp12
    • Protein or peptide: Non-structural protein 8
    • Protein or peptide: Non-structural protein 7
    • RNA: RNA Primer
    • RNA: RNA template
  • Ligand: ZINC ION
KeywordsIBV / Coronavirus / nsp12 / RdRp / RTC / Viral Protein
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / endonuclease activity ...Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / endonuclease activity / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Nonstructural protein 14, gammacoronavirus / Nonstructural protein 15, middle domain, gammacoronavirus / Nonstructural protein 15, N-terminal, gammacoronavirus / RNA-dependent RNA polymerase, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / Viral (Superfamily 1) RNA helicase ...Nonstructural protein 14, gammacoronavirus / Nonstructural protein 15, middle domain, gammacoronavirus / Nonstructural protein 15, N-terminal, gammacoronavirus / RNA-dependent RNA polymerase, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / Viral (Superfamily 1) RNA helicase / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesInfectious bronchitis virus / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHoferle PJ / Anderson TK / Kirchdoerfer RN
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158463 United States
CitationJournal: Biorxiv / Year: 2024
Title: A genus-specific nsp12 region impacts polymerase assembly in Alpha- and Gammacoronaviruses
Authors: Hoferle PJ / Anderson TK / Kirchdoerfer RN
History
DepositionJul 18, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45805.png

Downloads & links

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Map

FileDownload / File: emd_45805.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum-1.4769253 - 2.1568408
Average (Standard dev.)0.0016667 (±0.045570824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45805_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45805_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Core polymerase complex of the infectious bronchitis virus compos...

EntireName: Core polymerase complex of the infectious bronchitis virus composed of nsp12, nsp8, nsp7, and an dsRNA substrate
Components
  • Complex: Core polymerase complex of the infectious bronchitis virus composed of nsp12, nsp8, nsp7, and an dsRNA substrate
    • Protein or peptide: RNA-directed RNA polymerase nsp12
    • Protein or peptide: Non-structural protein 8
    • Protein or peptide: Non-structural protein 7
    • RNA: RNA Primer
    • RNA: RNA template
  • Ligand: ZINC ION

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Supramolecule #1: Core polymerase complex of the infectious bronchitis virus compos...

SupramoleculeName: Core polymerase complex of the infectious bronchitis virus composed of nsp12, nsp8, nsp7, and an dsRNA substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Infectious bronchitis virus
Molecular weightTheoretical: 194.379 KDa

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Macromolecule #1: RNA-directed RNA polymerase nsp12

MacromoleculeName: RNA-directed RNA polymerase nsp12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Infectious bronchitis virus
Molecular weightTheoretical: 107.473109 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: FDKNYLNRVR GSSEARLIPL ANGCDPDVVK RAFDVCNKES AGMFQNLKRN CARFQEVRDT EDGNLEYCDS YFVVKQTTPS NYEHEKACY EDLKSEVTAD HDFFVFNKNI YNISRQRLTK YTMMDFCYAL RHFDPKDCEV LKEILVTYGC IEDYHPKWFE E NKDWYDPI ...String:
FDKNYLNRVR GSSEARLIPL ANGCDPDVVK RAFDVCNKES AGMFQNLKRN CARFQEVRDT EDGNLEYCDS YFVVKQTTPS NYEHEKACY EDLKSEVTAD HDFFVFNKNI YNISRQRLTK YTMMDFCYAL RHFDPKDCEV LKEILVTYGC IEDYHPKWFE E NKDWYDPI ENPKYYAMLA KMGPIVRRAL LNAIEFGNLM VEKGYVGVIT LDNQDLNGKF YDFGDFQKTA PGAGVPVFDT YY SYMMPII AMTDALAPER YFEYDVHKGY KSYDLLKYDY TEEKQDLFQK YFKYWDQEYH PNCRDCSDDR CLIHCANFNI LFS TLVPQT SFGNLCRKVF VDGVPFIATC GYHSKELGVI MNQDNTMSFS KMGLSQLMQF VGDPALLVGT SNKLVDLRTS CFSV CALAS GITHQTVKPG HFNKDFYDFA EKAGMFKEGS SIPLKHFFYP QTGNAAINDY DYYRYNRPTM FDIRQLLFCL EVTSK YFEC YEGGCIPASQ VVVNNLDKSA GYPFNKFGKA RLYYEMSLEE QDQLFESTKK NVLPTITQMN LKYAISAKNR ARTVAG VSI LSTMTNRQFH QKILKSIVNT RNAPVVIGTT KFYGGWDNML RNLIQGVEDP ILMGWDYPKC DRAMPNLLRI AASLVLA RK HTNCCTWSER VYRLYNECAQ VLSETVLATG GIYVKPGGTS SGDATTAYAN SVFNIIQATS ANVARLLSVI TRDIVYDD I KSLQYELYQQ VYRRVNFDPA FVEKFYSYLC KNFSLMILSD DGVVCYNNTL AKQGLVADIS GFREVLYYQN NVFMADSKC WVEPDLEKGP HEFCSQHTML VEVDGEPRYL PYPDPSRILC ACVFVDDLDK TESVAVMERY IALAIDAYPL VHHENEEYKK VFFVLLSYI RKLYQELSQN MLMDYSFVMD IDKGSKFWEQ EFYENMYRAP T

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #2: Non-structural protein 8

MacromoleculeName: Non-structural protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Infectious bronchitis virus
Molecular weightTheoretical: 21.567691 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: FSHIPSYAEY ERAKSIYEKV LADSKNGGVT QQELAAYRKA ANIAKSVFDR DLAVQKKLDS MAERAMTTMY KEARVTDRRA KLVSSLHAL LFSMLKKIDS EKLNVLFDQA NSGVVPLATV PIVCSNKLTL VIPDPETWVK CVEGVHVTYS TVVWNIDCVT D ADGTELHP ...String:
FSHIPSYAEY ERAKSIYEKV LADSKNGGVT QQELAAYRKA ANIAKSVFDR DLAVQKKLDS MAERAMTTMY KEARVTDRRA KLVSSLHAL LFSMLKKIDS EKLNVLFDQA NSGVVPLATV PIVCSNKLTL VIPDPETWVK CVEGVHVTYS TVVWNIDCVT D ADGTELHP TSTGSGLTYC ISGDNIAWPL KVNLTRN

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #3: Non-structural protein 7

MacromoleculeName: Non-structural protein 7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Infectious bronchitis virus
Molecular weightTheoretical: 8.014378 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
KLSDVKCTTV VLMQLLTKLN VEANSKMHAY LVELHNKILA SDDVGECMDN LLGMLITLFC IDSTIDLGEY CD

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #4: RNA Primer

MacromoleculeName: RNA Primer / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 9.527713 KDa
SequenceString:
UCUCCUAAGA AGCUAUUAAA AUCACAGAUU

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Macromolecule #5: RNA template

MacromoleculeName: RNA template / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 10.566281 KDa
SequenceString:
AAAAAUCUGU GAUUUUAAUA GCUUCUUAGG AGA

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / 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

BufferpH: 8
GridModel: EMS Lacey Carbon / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 79000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 179183
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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