6M71: SARS-Cov-2 RNA-dependent RNA polymerase

SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors. Determined by electron microscopy at 2.9 Å resolution. Released 1 Apr 2020.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 4
Atoms: 8,614
Mol. weight: 161.22 kDa
Released: 1 Apr 2020

Explore 6M71 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M71 contains 58 α-helices and 48 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 46 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	33-38	6	1
β-strand	43-48	6	1
α-helix	77-89	13
β-strand	96	1	2
α-helix	97-98	2
β-strand	99-100	2	3
β-strand	115-116	2	3
β-strand	123	1	4
α-helix	124-132	9
α-helix	140-148	9
α-helix	154-158	5
α-helix	171-175	5
α-helix	176-178	3
α-helix	179-198	20
β-strand	201-202	2	5
β-strand	203-204	2	6
α-helix	207-209	3
β-strand	211	1	4
β-strand	216	1	2
β-strand	223-224	2	5
β-strand	232-233	2	6
α-helix	235-241	7
α-helix	243-247	5
α-helix	252-255	4
β-strand	256	1	7
α-helix	264	1
β-strand	265	1	7
α-helix	266	1
α-helix	276-286	11
α-helix	304-317	14
α-helix	318-320	3
α-helix	323-325	3
β-strand	327-335	9	8
β-strand	338-348	11	8
β-strand	352-354	3	8
β-strand	363	1	8
α-helix	368-375	8
α-helix	378-383	6
β-strand	386-390	5	9
α-helix	396	1
β-strand	397-400	4	9
β-strand	408	1	10
β-strand	410	1	11
β-strand	414-415	2	12
α-helix	417-425	9
β-strand	440	1	13
β-strand	444	1	11
β-strand	447	1	10
α-helix	449-453	5
α-helix	454-458	5
α-helix	466-479	14
α-helix	490-492	3
α-helix	506-508	3
α-helix	512-518	7
α-helix	521-531	11
β-strand	539-544	6	9
β-strand	549	1	13
β-strand	556-560	5	9
α-helix	562-580	19
β-strand	587	1	14
α-helix	597-605	9
β-strand	612-617	6	14
α-helix	622-625	4
α-helix	628-639	12
α-helix	648-658	11
α-helix	659-663	5
β-strand	666-669	4	9
β-strand	672-675	4	9
α-helix	687-708	22
α-helix	719-731	13
α-helix	739-752	14
β-strand	753-758	6	14
β-strand	761-767	7	14
α-helix	768-773	6
α-helix	779-790	12
β-strand	801-802	2	14
β-strand	816-821	6	15
β-strand	826-831	6	15
α-helix	834-842	9
β-strand	843-844	2	12
α-helix	852-866	15
α-helix	867-871	5
α-helix	875-894	20
α-helix	919-922	4
α-helix	923-925	3

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	79-95	17
α-helix	101-107	7
β-strand	114-116	3	8
α-helix	120-123	4
β-strand	127-132	6	9
α-helix	136-139	4
β-strand	147	1	9
β-strand	154-155	2	9
β-strand	160	1	9
β-strand	166	1	9
α-helix	183	1
β-strand	184-190	7	9

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-19	16
α-helix	22-24	3
α-helix	26-40	15
α-helix	45-60	16

Chain D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	86-98	13
α-helix	101-111	11
β-strand	116	1	16
α-helix	119-121	3
β-strand	130	1	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-directed RNA polymerase	A	protein	942	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)
Non-structural protein 7	C	protein	83	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)
Non-structural protein 8	B, D	protein	198	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6M71_1 RNA-directed RNA polymerase (chains A)
SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKD
EDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLT
KYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGE
RVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSL
LMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVN
CLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVN
LHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFY
DFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYF
DCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTIT
QMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHN
MLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECA
QVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV
RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIK
NFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGA
GCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHML
DMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQHHHHHHHHHH

Sequence of entity 2 (C), FASTA

>6M71_2 Non-structural protein 7 (chains C)
SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLL
SMQGAVDINKLCEEMLDNRATLQ

Sequence of entity 3 (B, D), FASTA

>6M71_3 Non-structural protein 8 (chains B, D)
AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLE
KMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNII
PLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNL
AWPLIVTALRANSAVKLQ

Primary citation

Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Gao, Y., Yan, L., Huang, Y. et al. Science (2020) 368:779-782. DOI 10.1126/science.abb7498 · PubMed

Other PDB entries of the same protein (UniProt P0DTD1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

44PS 0.77 Å, 6-conformation model of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
7KR0 0.77 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
9CY0 0.8 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-4206
7TX0 0.84 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43…
7KQO 0.85 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain (P43 crystal form)
7HCO 0.87 Å, PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in…
7KQP 0.88 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose (P43 crystal…
7TWJ 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 4 (P43 crystal form)
7TWN 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 5 (P43 crystal form)
7TWO 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 6 (P43 crystal form)
7TWP 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 7 (P43 crystal form)
7TWQ 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 9 (P43 crystal form)

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6M71 is part of these collections:

SARS-CoV-2 and COVID-19

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