Structure of PDB 7cyq Chain A

Receptor sequence

>7cyqA (length=926) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

AQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNC
CRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFK
FRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCD
DDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVG
VLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTA
ESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLD
DRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGV
VHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTN
NVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDY
DYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAG
FPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNR
ARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLK
TVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFY
RLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTAN
VNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHF
SMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTET
DLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGT
LMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMY
SVMLTNDNTSRYWEPEFYEAMYTPHT

3D structure

• PDB: 7cyq Cryo-EM Structure of an Extended SARS-CoV-2 Replication and Transcription Complex Reveals an Intermediate State in Cap Synthesis.
• Chain: A
• Resolution: 2.83 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	S759 C813 S814 R836 E857 R858 S861	S756 C810 S811 R833 E854 R855 S858
BS02	rna	A	K500 S501 V557 R569 K577 G590 S592 Y595 S682 G683 D684 A685 Y689 Y915 M924	K497 S498 V554 R566 K574 G587 S589 Y592 S679 G680 D681 A682 Y686 Y912 M921
BS03	ZN	A	H295 C301 C306 C310	H292 C298 C303 C307
BS04	ZN	A	C487 H642 C646	C484 H639 C643
BS05	GDP	A	N52 K73 H75 R116 D218	N49 K70 H72 R113 D215
BS06	MG	A	N209 D218	N206 D215

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0039694 viral RNA genome replication

External links

• PDB: RCSB:7cyq, PDBe:7cyq, PDBj:7cyq
• PDBsum: 7cyq
• PubMed: 33232691
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)