8WBY: ACE2-B0AT1 complex with JX98

Cryo-EM structure of ACE2-B0AT1 complex with JX98. Determined by electron microscopy at 3.18 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.18 Å
Organism: Homo sapiens
Chains: 4
Atoms: 22,232
Mol. weight: 341.12 kDa
Ligands: NAG, WM8
Released: 11 Sept 2024

Explore 8WBY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8WBY contains 150 α-helices and 32 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: 38 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	16-17	2
α-helix	18-24	7
α-helix	33-35	3
α-helix	38-54	17
α-helix	61-66	6
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-88	6
α-helix	92-96	5
α-helix	101-106	6
α-helix	114-141	28
α-helix	149-151	3
α-helix	153-154	2
β-strand	155	1	1
β-strand	162	1	1
α-helix	164-168	5
α-helix	171-174	4
α-helix	175-180	6
α-helix	195-211	17
α-helix	216-226	11
α-helix	229-242	14
α-helix	249-255	7
α-helix	259-263	5
α-helix	266-279	14
α-helix	285-290	6
α-helix	300-348	49
α-helix	360-370	11
α-helix	403-407	5
α-helix	413-445	33
α-helix	455-469	15
α-helix	472-474	3
α-helix	478-486	9
α-helix	492-507	16
α-helix	511-517	7
α-helix	518-522	5
α-helix	528-535	8
α-helix	538-552	15
α-helix	580-582	3
α-helix	583-589	7
α-helix	593-607	15

Chain B: 35 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	22-52	31
α-helix	57-78	22
α-helix	85-87	3
α-helix	91-99	9
α-helix	110-128	19
β-strand	132-133	2	2
β-strand	141-142	2	2
α-helix	144-148	5
α-helix	149-154	6
α-helix	158-192	35
α-helix	199-204	6
β-strand	209	1	3
β-strand	217	1	3
α-helix	221-248	28
β-strand	262-263	2	4
α-helix	264-266	3
α-helix	276-280	5
α-helix	294-299	6
α-helix	306-317	12
α-helix	325-329	5
β-strand	347-349	3	5
β-strand	357-359	3	5
α-helix	366-384	19
α-helix	390-392	3
α-helix	400-412	13
α-helix	415-421	7
α-helix	432-446	15
α-helix	450-464	15
α-helix	473-480	8
α-helix	481-485	5
β-strand	487-488	2	4
α-helix	499-502	4
α-helix	504-507	4
α-helix	514-533	20
α-helix	548-558	11
α-helix	566-571	6
α-helix	582-587	6
α-helix	589-598	10
β-strand	618-622	5	6
α-helix	624-628	5
α-helix	632-635	4
α-helix	637-657	21
β-strand	670-673	4	6
β-strand	680-685	6	6
β-strand	686	1	7
β-strand	694	1	7
α-helix	697-713	17
β-strand	722-723	2	6
α-helix	741-766	26

Chain C: 39 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	22-52	31
α-helix	56-58	3
α-helix	60-78	19
α-helix	92-100	9
α-helix	104-107	4
α-helix	110-129	20
β-strand	132	1	8
β-strand	142	1	8
α-helix	144-148	5
α-helix	149-154	6
α-helix	158-192	35
α-helix	199-204	6
β-strand	209	1	9
β-strand	217	1	9
α-helix	219-251	33
β-strand	262-263	2	10
α-helix	264-266	3
α-helix	276-278	3
α-helix	279-282	4
α-helix	289-291	3
α-helix	296-299	4
α-helix	304-317	14
α-helix	325-329	5
β-strand	347-350	4	11
β-strand	356-359	4	11
α-helix	366-384	19
α-helix	390-392	3
α-helix	400-412	13
α-helix	415-421	7
α-helix	432-446	15
α-helix	450-465	16
α-helix	473-480	8
α-helix	481-485	5
β-strand	487-488	2	10
α-helix	499-502	4
α-helix	504-507	4
α-helix	513-533	21
α-helix	539-541	3
α-helix	548-558	11
α-helix	566-571	6
α-helix	582-587	6
α-helix	589-598	10
β-strand	618-622	5	12
α-helix	624-628	5
α-helix	632-635	4
α-helix	637-657	21
β-strand	670-673	4	12
β-strand	680-685	6	12
β-strand	686-687	2	13
β-strand	690-694	5	13
α-helix	697-715	19
β-strand	722-723	2	12
α-helix	741-766	26

Chain D: 38 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	18-24	7
α-helix	38-54	17
α-helix	63-66	4
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-88	6
α-helix	92-96	5
α-helix	101-106	6
α-helix	113-141	29
α-helix	149-151	3
α-helix	153-154	2
β-strand	155	1	14
β-strand	162	1	14
α-helix	164-168	5
α-helix	171-174	4
α-helix	175-181	7
α-helix	195-211	17
α-helix	216-226	11
α-helix	229-242	14
α-helix	249-255	7
α-helix	260-263	4
α-helix	266-279	14
α-helix	285-290	6
α-helix	300-348	49
α-helix	360-370	11
α-helix	398-402	5
α-helix	403-407	5
α-helix	413-446	34
α-helix	455-469	15
α-helix	470-474	5
α-helix	478-489	12
α-helix	492-507	16
α-helix	511-521	11
α-helix	528-535	8
α-helix	538-541	4
α-helix	543-554	12
α-helix	580-582	3
α-helix	583-589	7
α-helix	592-595	4
α-helix	597-608	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent neutral amino acid transporter B(0)AT1	A, D	protein	651	Homo sapiens	Q695T7 (AlphaFold model)
Angiotensin-converting enzyme 2	B, C	protein	817	Homo sapiens	Q9BYF1 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8WBY_1 Sodium-dependent neutral amino acid transporter B(0)AT1 (chains A, D)
DYKDDDDKSGPDEVDASGVRLVLPNPGLDARIPSLAELETIEQEEASSRPKWDNKAQYML
TCLGFCVGLGNVWRFPYLCQSHGGGAFMIPFLILLVLEGIPLLYLEFAIGQRLRRGSLGV
WSSIHPALKGLGLASMLTSFMVGLYYNTIISWIMWYLFNSFQEPLPWSDCPLNENQTGYV
DECARSSPVDYFWYRETLNISTSISDSGSIQWWMLLCLACAWSVLYMCTIRGIETTGKAV
YITSTLPYVVLTIFLIRGLTLKGATNGIVFLFTPNVTELAQPDTWLDAGAQVFFSFSLAF
GGLISFSSYNSVHNNCEKDSVIVSIINGFTSVYVAIVVYSVIGFRATQRYDDCFSTNILT
LINGFDLPEGNVTQENFVDMQQRCNASDPAAYAQLVFQTCDINAFLSEAVEGTGLAFIVF
TEAITKMPLSPLWSVLFFIMLFCLGLSSMFGNMEGVVVPLQDLRVIPPKWPKEVLTGLIC
LGTFLIGFIFTLNSGQYWLSLLDSYAGSIPLLIIAFCEMFSVVYVYGVDRFNKDIEFMIG
HKPNIFWQVTWRVVSPLLMLIIFLFFFVVEVSQELTYSIWDPGYEEFPKSQKISYPNWVY
VVVVIVAGVPSLTIPGYAIYKLIRNHCQKPGDHQGLVSTLSTASMNGDLKY

Sequence of entity 2 (B, C), FASTA

>8WBY_2 Angiotensin-converting enzyme 2 (chains B, C)
MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQ
NMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTIL
NTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLY
EEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHL
HAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQ
AWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILM
CTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKS
IGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEM
KREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLH
KCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNK
NSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKN
QMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDN
SLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENP
YASIDISKGENNPGFQNTDDVQTSFLEHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
WM8	2-(4-chloranyl-3,5-dimethyl-phenoxy)-~{N}-propan-2-yl-ethanamide	C13 H18 Cl N O2	2

Primary citation

Molecular basis of inhibition of the amino acid transporter B 0 AT1 (SLC6A19). Xu, J., Hu, Z., Dai, L. et al. Nat Commun (2024) 15:7224-7224. DOI 10.1038/s41467-024-51748-1 · 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
6M17 2.9 Å, The 2019-nCoV RBD/ACE2-B0AT1 complex
6M18 2.9 Å, ACE2-B0AT1 complex

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