Viral protein-Nucleic acid complex

Macro molecule
Gene
Interacting molecule/ protein
Interacting gene
PDB ID
Title
Structure Title
Experimental Method
Resolution (Å)
PubMed ID
Structure
NSP12, NSP8,NSP7
rep, 1a-1b
RNA (5'-R(P*UP*UP*AP*AP*GP*UP*UP*AP*U)-3') RNA (5'-R(P*UP*UP*CP*AP*UP*AP*AP*CP*UP*UP*AP*A)-3')
~
7AAP
Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP
Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP
ELECTRON MICROSCOPY
2.5
To be published
3D view
Nucleoprotein
N
10mer ssRNA
~
7ACT
Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein.
The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 10mer ssRNA
SOLUTION NMR
~
33264373
3D view
Nucleoprotein
N
RNA (5'-R(P*CP*AP*CP*UP*GP*AP*C)-3') RNA (5'-R(P*GP*UP*CP*AP*GP*UP*G)-3')
~
7ACS
The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 7mer ssRNA
The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 7mer dsRNA
SOLUTION NMR
~
33264373
3D view
Nsp12, Nsp8, Nsp7
rep, 1a-1b
RNA product
~
6YYT
Structure of replicating SARS-CoV-2 polymerase.
Structure of replicating SARS-CoV-2 polymerase
ELECTRON MICROSCOPY
2.9
32438371
3D view
RNA-directed RNA polymerase, nsp8, nsp7
rep, 1a-1b
RNA (5'-R(*GP*UP*GP*GP*GP*CP*CP*CP*A)-3')
~
6XQB
Structure of SARS-CoV-2 RdRp/RNA complex at 3.4 Angstroms resolution
SARS-CoV-2 RdRp/RNA complex
ELECTRON MICROSCOPY
3.4
To be published
3D view
RNA-directed RNA polymerase, nsp8, nsp7
rep, 1a-1b
RNA (31-MER)
~
7BZF
Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase.
COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex
ELECTRON MICROSCOPY
3.26
32526208
3D view
Nsp12, Nsp8,NSP7
rep, 1a-1b
Favipiravir Primer-RNA (5'-R(P*UP*UP*CP*UP*CP*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*A)-3') Template-RNA (5'-R(P*AP*CP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*GP*GP*AP*GP*AP*A)-3')
~
7CTT
Cryo-EM structure of Favipiravir bound to replicating polymerase complex of SARS-CoV-2 in the pre-catalytic state.
Cryo-EM structure of Favipiravir bound to replicating polymerase complex of SARS-CoV-2 in the pre-catalytic state.
ELECTRON MICROSCOPY
3.2
To be published
3D view
Nsp7, Nsp8 , Nsp13,
rep, 1a-1b
RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
~
7CXN
Architecture of a SARS-CoV-2 mini replication and transcription complex.
Architecture of a SARS-CoV-2 mini replication and transcription complex
ELECTRON MICROSCOPY
3.84
33208736
3D view
Nsp7, Nsp8 , Nsp12, Nsp13
RNA (25-MER) RNA (26-MER) RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
~
7CXM
Architecture of a SARS-CoV-2 mini replication and transcription complex.
Architecture of a SARS-CoV-2 mini replication and transcription complex
ELECTRON MICROSCOPY
2.9
33208736
3D view
Replicase polyprotein 1ab, Nsp7, Nsp8
rep, 1a-1b
Template
~
7CYQ
Cryo-EM Structure of an Extended SARS-CoV-2 Replication and Transcription Complex Reveals an Intermediate State in Cap Synthesis.
Cryo-EM structure of an extended SARS-CoV-2 replication and transcription complex reveals an intermediate state in cap synthesis
ELECTRON MICROSCOPY
2.83
33232691
3D view
Nsp10, 2'-O-methyltransferase
rep, 1a-1b
2'-O-methylated m7GpppA Cap-1 and SAH
~
7JHE
Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with 2'-O-methylated m7GpppA Cap-1 and SAH Determined by Fixed-Target Serial Crystallography
Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with 2'-O-methylated m7GpppA Cap-1 and SAH Determined by Fixed-Target Serial Crystallography
X-RAY DIFFRACTION
2.25
To be published
3D view
Nsp10, Nsp16
rep, 1a-1b
Substrates and Products of 2'-O-methylation of the Cap-1
~
7JIB
Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of 2'-O-methylation of the Cap-1
Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of 2'-O-methylation of the Cap-1
X-RAY DIFFRACTION
2.65
To be published
3D view
Nsp10
rep, 1a-1b
2'-O-methyltransferase RNA (5'-D(*(M7G))-R(P*AP*UP*UP*A)-3')
~
7JYY
Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA (Cap-0) and S-Adenosylmethionine (SAM).
Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA (Cap-0) and S-Adenosylmethionine (SAM).
X-RAY DIFFRACTION
2.05
To be published
3D view
Nsp10
rep, 1a-1b
2'-O-methyltransferase RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*U)-3')
~
7JZ0
Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1) and S-Adenosyl-L-homocysteine (SAH).
Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1) and S-Adenosyl-L-homocysteine (SAH).
X-RAY DIFFRACTION
2.15
To be published
3D view
3C-like proteinase
rep, 1a-1b
C-terminal autoprocessing sequence.
~
7KHP
Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.
Acyl-enzyme intermediate structure of SARS-CoV-2 Mpro in complex with its C-terminal autoprocessing sequence.
X-RAY DIFFRACTION
1.95
33208735
3D view
Uridylate-specific endoribonuclease
rep, 1a-1b
DNA (5'-R(*GP*U)-3')
~
6X1B
Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.
X-RAY DIFFRACTION
1.97
To be published
3D view