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Basic information

Entry
Database: PDB / ID: 2ahm
TitleCrystal structure of SARS-CoV super complex of non-structural proteins: the hexadecamer
Components
  • Replicase polyprotein 1ab, heavy chain
  • Replicase polyprotein 1ab, light chain
KeywordsViral protein / Replication / SARS-CoV / coronavirus / non-structural protein / nsp7 / nsp8 / super-complex / hexadecamer
Function / homology
Function and homology information


positive regulation of ubiquitin-specific protease activity / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Lys48-specific deubiquitinase activity / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / 7-methylguanosine mRNA capping / mRNA (guanine-N7-)-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases ...positive regulation of ubiquitin-specific protease activity / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Lys48-specific deubiquitinase activity / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / 7-methylguanosine mRNA capping / mRNA (guanine-N7-)-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / 5'-3' RNA helicase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / Lyases; Phosphorus-oxygen lyases / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / suppression by virus of host type I interferon production / SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / 3'-5'-exoribonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / G-quadruplex RNA binding / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host ISG15-protein conjugation / protein K48-linked deubiquitination / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transcription, RNA-templated / suppression by virus of host NF-kappaB cascade / viral transcription / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive stranded viral RNA replication / protein autoprocessing / viral genome replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host TRAF activity / helicase activity / ubiquitinyl hydrolase 1 / double-stranded RNA binding / DNA helicase / thiol-dependent deubiquitinase / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / suppression by virus of host type I interferon-mediated signaling pathway / transcription, DNA-templated / host cell cytoplasm / protein dimerization activity / : / endoplasmic reticulum membrane / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2820 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #580 / nsp7 replicase / Nsp8 replicase, head domain / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase, Ruva Protein; domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 14, betacoronavirus ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2820 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #580 / nsp7 replicase / Nsp8 replicase, head domain / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase, Ruva Protein; domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 14, betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Non-structural protein NSP16, coronavirus-like / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Non-structural protein 14, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Sarbecovirus Nsp3c-N domain profile. / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus SUD-C domain / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Betacoronavirus Nsp3c-M domain profile. / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP1, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein 6, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP3, C-terminal / Coronavirus endopeptidase C30 / Coronavirus replicase NSP6 / Coronavirus papain-like peptidase / Coronavirus replicase NSP4, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP8 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, N-terminal / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein 6, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsZhai, Y.J. / Sun, F. / Bartlam, M. / Rao, Z.
CitationJournal: NAT.STRUCT.MOL.BIOL. / Year: 2005
Title: Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer
Authors: Zhai, Y.J. / Sun, F. / Li, X. / Pang, H. / Xu, X. / Bartlam, M. / Rao, Z.
History
DepositionJul 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicase polyprotein 1ab, light chain
B: Replicase polyprotein 1ab, light chain
C: Replicase polyprotein 1ab, light chain
D: Replicase polyprotein 1ab, light chain
E: Replicase polyprotein 1ab, heavy chain
F: Replicase polyprotein 1ab, heavy chain
G: Replicase polyprotein 1ab, heavy chain
H: Replicase polyprotein 1ab, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,50714
Polymers127,9518
Non-polymers5576
Water2,684149
1
A: Replicase polyprotein 1ab, light chain
B: Replicase polyprotein 1ab, light chain
C: Replicase polyprotein 1ab, light chain
D: Replicase polyprotein 1ab, light chain
E: Replicase polyprotein 1ab, heavy chain
F: Replicase polyprotein 1ab, heavy chain
G: Replicase polyprotein 1ab, heavy chain
H: Replicase polyprotein 1ab, heavy chain
hetero molecules

A: Replicase polyprotein 1ab, light chain
B: Replicase polyprotein 1ab, light chain
C: Replicase polyprotein 1ab, light chain
D: Replicase polyprotein 1ab, light chain
E: Replicase polyprotein 1ab, heavy chain
F: Replicase polyprotein 1ab, heavy chain
G: Replicase polyprotein 1ab, heavy chain
H: Replicase polyprotein 1ab, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,01528
Polymers255,90216
Non-polymers1,11312
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area53670 Å2
ΔGint-452 kcal/mol
Surface area90680 Å2
MethodPISA, PQS
Unit cell
γ
α
β
Length a, b, c (Å)93.6, 94.0, 150.8
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-2034-

HOH

DetailsThe biological assembly is a hexadecamer generated from the octamer in the asymmetric unit by the operations: 1-x, 1-y, z.

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Components

#1: Protein
Replicase polyprotein 1ab, light chain / replicase nsp7


Mass: 9688.271 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Plasmid: pGEX6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P59641, UniProt: P0C6X7*PLUS
#2: Protein
Replicase polyprotein 1ab, heavy chain / replicase nsp8


Mass: 22299.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Plasmid: pGEX6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P59641, UniProt: P0C6X7*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulfate, Sodium Chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBSRF 3W1A10.9791, 0.9793, 0.9500
SYNCHROTRONAPS 19-ID21.0332
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJan 17, 2005
ADSC QUANTUM 42CCDFeb 10, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)MADMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.951
41.03321
ReflectionResolution: 2.3→50 Å / Num. obs: 58479 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 24
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4881 / % possible all: 82

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 5209 -RANDOM
Rwork0.213 ---
all0.26 52765 --
obs0.232 51504 97.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7598 0 35 149 7782
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.136
X-RAY DIFFRACTIONc_dihedral_angle_d20.162
X-RAY DIFFRACTIONc_improper_angle_d0.731

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