Structure of PDB 7rdy Chain A

Receptor sequence

>7rdyA (length=927) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

DAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTN
CCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFF
KFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCC
DDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIV
GVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALT
AESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCL
DDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELG
VVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALT
NNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISD
YDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSA
GFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKN
RARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNML
KTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRF
YRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTA
NVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKH
FSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTE
TDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDG
TLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDM
YSVMLTNDNTSRYWEPEFYEAMYTPHT

3D structure

• PDB: 7rdy Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex.
• Chain: A
• Resolution: 3.1 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 D760 D761 C813 S814 R836 K849 R858 S861	S757 D758 D759 C811 S812 R834 K847 R856 S859
BS02	rna	A	Q408 K500 S501 N543 V557 R569 K577 G590 S592 F594 S682 G683 D684 A685 Y689 Y915	Q406 K498 S499 N541 V555 R567 K575 G588 S590 F592 S680 G681 D682 A683 Y687 Y913
BS03	ZN	A	H295 C301 C306	H293 C299 C304
BS04	ZN	A	C487 H642 C646	C485 H640 C644
BS05	MG	A	N209 D218	N207 D216
BS06	ADP	A	F35 N52 H75 N79 R116 D218 G220	F33 N50 H73 N77 R114 D216 G218
BS07	1N7	A	V204 I223	V202 I221
BS08	1N7	A	R197 V231 Y289	R195 V229 Y287
BS09	1N7	A	Y903 V905	Y901 V903

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:7rdy, PDBe:7rdy, PDBj:7rdy
• PDBsum: 7rdy
• PubMed: 35260847
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)