6M17: The 2019-nCoV RBD/ACE2-B0AT1 complex

The 2019-nCoV RBD/ACE2-B0AT1 complex. Determined by electron microscopy at 2.9 Å resolution. Released 11 Mar 2020.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 6
Atoms: 25,344
Mol. weight: 394.14 kDa
Ligands: NAG, LEU, ZN
Released: 11 Mar 2020

Explore 6M17 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M17 contains 166 α-helices and 56 β-strands across 6 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.

Chains A and C: 33 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
α-helix	38-48	11
α-helix	58-64	7
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-96	14
α-helix	101-104	4
α-helix	113-141	29
β-strand	155	1	1
β-strand	162	1	1
α-helix	164-168	5
α-helix	173-175	3
α-helix	176-180	5
α-helix	196-211	16
α-helix	219-241	23
α-helix	251-255	5
α-helix	259-263	5
α-helix	266-278	13
α-helix	285-290	6
α-helix	301-316	16
α-helix	318-345	28
α-helix	360-370	11
α-helix	403-407	5
α-helix	415-429	15
α-helix	431-444	14
α-helix	455-469	15
α-helix	470-473	4
α-helix	478-504	27
α-helix	505-510	6
α-helix	511-521	11
α-helix	528-532	5
α-helix	533-537	5
α-helix	538-545	8
α-helix	547-553	7
β-strand	559-562	4	2
β-strand	574-577	4	2
α-helix	582-608	27

Chains B and D: 43 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	22-52	31
α-helix	59-80	22
α-helix	91-101	11
α-helix	110-128	19
β-strand	132-134	3	3
β-strand	137-142	6	3
α-helix	148-154	7
α-helix	158-192	35
α-helix	199-203	5
α-helix	204-207	4
β-strand	209	1	4
β-strand	217	1	4
α-helix	221-230	10
α-helix	234-251	18
β-strand	260	1	5
α-helix	261	1
β-strand	262-263	2	6
α-helix	276-278	3
α-helix	279-282	4
α-helix	289-291	3
α-helix	295-298	4
α-helix	304-318	15
α-helix	321-323	3
α-helix	327-330	4
β-strand	332	1	7
β-strand	347-352	6	7
β-strand	355-359	5	7
α-helix	366-382	17
α-helix	390-392	3
α-helix	400-412	13
α-helix	415-420	6
α-helix	432-443	12
α-helix	450-465	16
α-helix	470-472	3
α-helix	473-480	8
α-helix	481-485	5
β-strand	487-488	2	6
α-helix	500-502	3
α-helix	504-507	4
α-helix	514-532	19
α-helix	539-541	3
α-helix	549-558	10
α-helix	566-571	6
α-helix	582-587	6
α-helix	589-598	10
β-strand	607	1	5
β-strand	618-622	5	8
α-helix	624-627	4
α-helix	632-634	3
α-helix	637-657	21
α-helix	667-669	3
β-strand	670-673	4	8
β-strand	680-685	6	8
β-strand	686	1	9
β-strand	694	1	9
α-helix	695-696	2
α-helix	697-706	10
α-helix	708-715	8
β-strand	722-724	3	8
α-helix	741-765	25

Chains E and F: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	339-343	5
β-strand	356-358	3	10
α-helix	365-369	5
β-strand	376-379	4	10
α-helix	384-389	6
β-strand	394-402	9	10
α-helix	407-409	3
α-helix	417-421	5
β-strand	432-437	6	10
α-helix	439-442	4
β-strand	448-454	7	11
α-helix	460-462	3
β-strand	492-497	6	11
β-strand	508-516	9	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent neutral amino acid transporter B(0)AT1	A, C	protein	654	Homo sapiens	Q695T7 (AlphaFold model)
Angiotensin-converting enzyme 2	B, D	protein	814	Homo sapiens	Q9BYF1 (AlphaFold model)
Spike protein S1	E, F	protein	223	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6M17_1 Sodium-dependent neutral amino acid transporter B(0)AT1 (chains A, C)
MADYKDDDDKSGPDEVDASGRVRLVLPNPGLDARIPSLAELETIEQEEASSRPKWDNKAQ
YMLTCLGFCVGLGNVWRFPYLCQSHGGGAFMIPFLILLVLEGIPLLYLEFAIGQRLRRGS
LGVWSSIHPALKGLGLASMLTSFMVGLYYNTIISWIMWYLFNSFQEPLPWSDCPLNENQT
GYVDECARSSPVDYFWYRETLNISTSISDSGSIQWWMLLCLACAWSVLYMCTIRGIETTG
KAVYITSTLPYVVLTIFLIRGLTLKGATNGIVFLFTPNVTELAQPDTWLDAGAQVFFSFS
LAFGGLISFSSYNSVHNNCEKDSVIVSIINGFTSVYVAIVVYSVIGFRATQRYDDCFSTN
ILTLINGFDLPEGNVTQENFVDMQQRCNASDPAAYAQLVFQTCDINAFLSEAVEGTGLAF
IVFTEAITKMPLSPLWSVLFFIMLFCLGLSSMFGNMEGVVVPLQDLRVIPPKWPKEVLTG
LICLGTFLIGFIFTLNSGQYWLSLLDSYAGSIPLLIIAFCEMFSVVYVYGVDRFNKDIEF
MIGHKPNIFWQVTWRVVSPLLMLIIFLFFFVVEVSQELTYSIWDPGYEEFPKSQKISYPN
WVYVVVVIVAGVPSLTIPGYAIYKLIRNHCQKPGDHQGLVSTLSTASMNGDLKY

Sequence of entity 2 (B, D), FASTA

>6M17_2 Angiotensin-converting enzyme 2 (chains B, D)
MRSSSSWLLLSLVAVTAAWSHPQFEKQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYN
TNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSED
KSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSE
VGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFE
EIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNI
DVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDL
GKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLS
AATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKD
QWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQ
AAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPL
FTWLKDQNKNSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAM
RQYFLKVKNQMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRI
NDAFRLNDNSLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKK
NKARSGENPYASIDISKGENNPGFQNTDDVQTSF

Sequence of entity 3 (E, F), FASTA

>6M17_3 Spike protein S1 (chains E, F)
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFK
CYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNS
NNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQ
PTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10
LEU	Leucine	C6 H13 N O2	2
ZN	Zinc ion	Zn	2

Primary citation

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Yan, R., Zhang, Y., Li, Y. et al. Science (2020) 367:1444-1448. DOI 10.1126/science.abb2762 · PubMed

Other PDB entries of the same protein (UniProt Q695T7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9KXW 2.66 Å, Structure of human B0AT1-ACE2
9KY0 2.68 Å, Structure of human B0AT1-ACE2 complex with compound3
9KXT 2.7 Å, Structure of human B0AT1-ACE2 complex with compound1
9KXV 2.71 Å, Structure of human B0AT1-ACE2 complex with compound3
9KXX 2.77 Å, Inward-open Structure of human B0AT1
9KXZ 2.8 Å, Structure of human B0AT1-ACE2 complex with compound1
9KY1 2.8 Å, Structure of human B0AT1-ACE2 complex with compound1
9KXY 2.82 Å, Structure of human B0AT1-ACE2 complex with compound1
9KXU 2.87 Å, Structure of human B0AT1-ACE2 complex with compound 2
9VA2 2.87 Å, Structure of the ACE2-B0AT1 bound with Phenylalanine
6M18 2.9 Å, ACE2-B0AT1 complex
8I93 3.1 Å, ACE2-B0AT1 complex bound with methionine

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6M17 is part of these collections:

SARS-CoV-2 and COVID-19

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