Was ist die Datenbank?
Unsere Datenbank beinhaltet die makromolekularen Modelle der SARS-CoV und SARS-CoV-2 Proteine sowie die wichtigsten Strukturen menschlicher Coronavirus-Interaktionspartner. Hier finden Sie tausende experimentell bestimmte makromolekulare Strukturen — Originaldateien sowie neu prozessierte und modellierte Strukturen.
Alle Strukturen sind evaluiert worden. Zusatzlich wurden einige Strukturen händisch überprüft (siehe grüner Haken bei "Refinement"). Wenn wir dabei eine signifikante Verbesserung der Strukturen erreichen konnten, haben wir das verbesserte* Modell ebenfalls in der Datenbank.
*Diese Verbesserung stellt natürlich keinerlei Kritik an den herausragenden Leistungen anderer Forschungsgruppen dar; es geht darum, die Grenzen unserer modernen Methoden auszureizen, um jedes Bisschen biologischer Informationen zu extrahieren.
Unsere Datenbank ist eine globale und öffentliche Ressource für die makromolekularen Strukturen aus beta-Coronaviren, insbesondere SARS-CoV and SARS-CoV-2. Forschende können unsere Erkenntnisse nutzen, um die Viren und bestimmte Strukturen besser zu verstehen und Wirkstoffe gegen COVID-19 zu entwickeln.
Wo finde ich die Datenbank?
Neben der Tabelle am Seitenende kann die Datenbank über unser GitHub repository abgerufen werden. Informationen zur Beschaffenheit der Daten finden Sie hier.
Methodik
Die Vorgehensweise und Erklärungen zu unserer Forschung werden unter "Das Vorgehen" erklärt. "Auswahl der richtigen Struktur" gibt Hilfestellungen zur Bewertung der Strukturen und "Qualitätsindikatoren" einen Überblick über gängige Kriterien.
Die Daten
Image
PDB
Protein
Description
Preview
Github-Link
Refinement
Method
Resolution
R(work)
R(free)
Virus
6m03
nsp5 / 3c_like_proteinase
Full length 3C-like protease from SARS-CoV. This X-ray crystal structure was phased using PDB entry 6lu7 for molecular replacement & has data to a resolution of 1.99Å.
X-RAY DIFFRACTION
1.99 Å
0.1962
0.2458
SARS-CoV-2
2ozk
nsp15 / endornase
A truncated SARS-CoV Nsp15 (endoribonuclease) from residue 28-355 featuring a truncated N-terminal oligomerisation domain, the middle domain, and the catalytic NendoU domain at the C-terminal. The model contains four Nsp15 monomers and is unable to produce the full biological assembly (a hexamer consisting of a dimer of trimers) though generation of symmetry mates. This X-ray crystal structure has data to a resolution of 2.90Å.
X-RAY DIFFRACTION
2.9 Å
0.24337
0.30068
SARS-CoV
6vww
nsp15 / endornase
Full length SARS-CoV-2 Nsp15 (endoribonuclease) featuring an N-terminal oligomerisation domain, the middle domain, and the catalytic NendoU domain at the C-terminal. The model contains two Nsp15 monomers, one from each of the two trimers, which can be used to produce the full biological assembly (a hexamer consisting of a dimer of trimers) though generation of symmetry mates. This protein is bound to two magnesium ions not related to the active site. This X-ray crystal structure has data to a resolution of 2.20Å.
X-RAY DIFFRACTION
2.2 Å
0.1577
0.1777
SARS-CoV-2
6w01
nsp15 / endornase
Full length SARS-CoV-2 Nsp15 (endoribonuclease)featuring an N-terminal oligomerisation domain, the middle domain, and the catalytic NendoU domain at the C-terminal. The model contains two Nsp15 monomers, one from each of the two trimers, which can be used to produce the full biological assembly (a hexamer consisting of a dimer of trimers) though generation of symmetry mates. This protein is bound to a citrate molecule. This X-ray crystal structure has data to a resolution of 1.90Å.
X-RAY DIFFRACTION
1.9 Å
0.1605
0.1849
SARS-CoV-2
5c8t
nsp14-nsp10
Exonuclease (NSP14) in complex with NSP10 from SARS-CoV. This X-ray crystal structure was phased using single-wavelength anomalous dispersion to 3.2Å resolution. This model has a SAM present as a functional ligand. Exonuclease has two domains responsible for guanine-N7-methyltransferase & 3'-5' exoribonuclease activity with a flexible linker between. NSP10 acts as an activator protein for NSP14.
X-RAY DIFFRACTION
3.2 Å
0.2427
0.2646
SARS-CoV
5nfy
nsp14-nsp10
Exonuclease (NSP14) in complex with NSP10 from SARS-CoV. This X-ray crystal structure was phased using multi-wavelength anomalous dispersion to 3.38Å resolution. Exonuclease has two domains responsible for guanine-N7-methyltransferase & 3'-5' exoribonuclease activity with a flexible linker between. NSP10 acts as an activator protein for NSP14.
X-RAY DIFFRACTION
3.382 Å
0.1926
0.2349
SARS-CoV
6jyt
nsp13 / helicase
Full length structure of Helicase (NSP13) from SARS-CoV. This X-ray crystal structure was phased using single-wavelength anomalous dispersion to 2.8Å resolution. Helicase is a 5 domain protein responsible for the unwinding & separation of double stranded RNA & DNA with a 5'-3' polarity with an N-terminal zinc binding domain.
X-RAY DIFFRACTION
2.69 Å
0.2375
0.2925
SARS-CoV
1r42
..
Cryo-EM structure of an extended SARS-CoV-2 replication and transcription complex (RTC) reveals an intermediate state in cap structure synthesis. Cryo-EM structure of an extended RTC assembled by nsp7-nsp8 2 -nsp12-nsp13 2 -RNA and a single RNA-binding protein, nsp9. Nsp9 binds tightly to nsp12 (RdRp) NiRAN, allowing nsp9 N terminus inserting into the catalytic center of nsp12 NiRAN, which then inhibits activity.
X-RAY DIFFRACTION
2.2 Å
0.235
0.287
pdb\human_interaction_partners\ACE2
6m0j
spike protein / surface_glycoprotein
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2. This structure highlights the key interaction between the spike and ACE2, later confirmed by EM structures.
X-RAY DIFFRACTION
2.45 Å
0.192
0.2269
SARS-CoV-2
6m17
spike protein / surface_glycoprotein
Receptor binding domain in complex with full lenght ACE2 and amino acid transporter B0AT1. Study highlight the entry mechanism of SARS-CoV-2 in cells.
ELECTRON MICROSCOPY
2.9 Å
---
---
SARS-CoV-2
6vw1
spike protein / surface_glycoprotein
Chimeric receptor-binding domain where the binding site contains a loop and core domain from SARS and RBD SARS-CoV2, complexed with its receptor human ACE2.
X-RAY DIFFRACTION
2.68 Å
0.197
0.2288
SARS-CoV-2
1xak
hypothetical_protein_sars7a
SARS-CoV ORF7a accessory protein, a unique type I transmembrane protein of unknown function. Has a short cytoplasmic tail and a transmembrane domain. Consists of one chain (chain A), that forms a compact seven-stranded beta sandwich.
X-RAY DIFFRACTION
1.8 Å
0.223
0.275
SARS-CoV
6zm7
nsp1 / leader_protein
This electron microscopy structure shows the SARS-CoV-2 leader protein (Nsp1) in a complex human CCDC124-80S-EBP1 ribosome. The protein inserts its C-terminal domain into the mRNA channel of the ribosome, where it interferes with mRNA binding and inhibits translation. Nsp1 effectively blocks retinoic acid-inducible gene I-dependent innate immune responses that would otherwise facilitate clearance of the infection.
ELECTRON MICROSCOPY
2.7 Å
---
---
SARS-CoV-2
3r24
nsp16-nsp10
nsp16-nsp10 SARS coronavirus complex or SARS-CoV 2'-O-MTase bound with methyl donor SAM. The structure the interaction interface shows that nsp10 may stabilize the SAM-binding pocket and extend the RNA-binding groove of nsp16, which suggests that the nsp16/nsp10 interface may represent a beter drug target than the viral MTase active site fordeveloping highly specific anti-coronavirus drugs.
X-RAY DIFFRACTION
2 Å
0.193
0.222
SARS-CoV
6vxs
nsp3
2 Å Crystal Structure of Mac1 domain of NSP3 from SARS CoV-2. This domain has a function as an ADP ribose 1"-phosphatase.
X-RAY DIFFRACTION
2.01 Å
0.1864
0.2335
SARS-CoV-2
6w9c
nsp3
2.7 Å crystal structure of papain-like protease of SARS CoV-2. Pl2pro is responsible for the cleaving of nsp1 to nsp4 of the polyprotein and also has a role in reducing the human immune response.
X-RAY DIFFRACTION
2.7 Å
0.235
0.2791
SARS-CoV-2
6w4b
nsp9
This X-ray crystal structure of SARS-CoV2 RNA-replicase (NSP9) was phased using PDB entry 1uw7 for molecular replacement & has data to a resolution of 2.95Å. This protein has a unique fold forming a dimer through a GXXXG motif which is biologically important & seen in solution.
X-RAY DIFFRACTION
2.9 Å
0.2398
0.276
SARS-CoV-2
6m3m
nucleocapsid_protein
This Crystal structure shows the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein (N). It consists of four identical monomers. The structure displays a great overall similarity to other nucleocapsid protein N-terminal domains, but exhibits a unique potential RNA binding pocket alongside the β -sheet core.
X-RAY DIFFRACTION
2.7 Å
0.2578
0.2934
SARS-CoV-2
6vyo
nucleocapsid_protein
This Crystal structure shows the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein (N). The structure consists of four identical monomers and exhibits interactions with the ligands Cl-, Zn2+, Glycerol, and 2-(N-Morpholino)-Ethanesulfonic Acid. The N-terminal domain provides structural features for RNA binding.
X-RAY DIFFRACTION
1.7 Å
0.1592
0.2053
SARS-CoV-2
6nur
nsp7-nsp8-nsp12
SARS-CoV RNA Polymerase (NSP12) bound with NSP7 & two NSP8 co-factors. This electron microscopy model has 3.1Å resolution and was published alongside PDB entry 6nus.The NSP12 & NSP8 chains have some N-terminal truncations & NSP7 is full length. The NSP12-NSP7-NSP8 complex replicates viral RNA.
ELECTRON MICROSCOPY
3.1 Å
---
---
SARS-CoV
Die gesamte Tabelle gibt es auch hier:
https://github.com/thorn-lab/coronavirus_structural_task_force/blob/master/utils/database/stats.db