8WBZ: ACE2-B0AT1 complex with JX225

Cryo-EM structure of ACE2-B0AT1 complex with JX225. Determined by electron microscopy at 3.2 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 22,342
Mol. weight: 342.91 kDa
Ligands: XF0, NAG
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

8WBZ contains 159 α-helices and 40 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: 41 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	18-25	8
α-helix	38-53	16
α-helix	58-64	7
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-92	10
α-helix	100-106	7
α-helix	113-128	16
α-helix	132-141	10
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	229-241	13
α-helix	250-255	6
α-helix	259-263	5
α-helix	266-278	13
α-helix	286-290	5
α-helix	299-348	50
α-helix	360-370	11
α-helix	375-377	3
α-helix	397	1
α-helix	398-403	6
α-helix	404-409	6
α-helix	413-437	25
α-helix	441-445	5
α-helix	455-470	16
α-helix	471-474	4
α-helix	478-488	11
α-helix	492-505	14
α-helix	506-510	5
α-helix	511-521	11
α-helix	528-532	5
α-helix	533-537	5
α-helix	538-552	15
β-strand	561	1	2
β-strand	575	1	2
α-helix	582-587	6
α-helix	593-595	3
α-helix	596-607	12

Chain B: 41 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	22-52	31
α-helix	59-76	18
α-helix	77-79	3
α-helix	91-101	11
α-helix	104-107	4
α-helix	110-128	19
β-strand	132-133	2	3
β-strand	141-142	2	3
α-helix	144-148	5
α-helix	149-154	6
α-helix	158-168	11
α-helix	169-173	5
α-helix	174-192	19
α-helix	199-204	6
β-strand	209	1	4
β-strand	217	1	4
α-helix	219-231	13
α-helix	234-251	18
β-strand	260	1	5
α-helix	261	1
β-strand	262-263	2	6
α-helix	264-266	3
α-helix	276-281	6
α-helix	294-300	7
α-helix	306-317	12
α-helix	320-324	5
α-helix	325-329	5
β-strand	332	1	7
β-strand	347-352	6	7
β-strand	355-359	5	7
α-helix	366-384	19
α-helix	400-412	13
α-helix	415-420	6
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	6
α-helix	499-502	4
α-helix	504-507	4
α-helix	514-532	19
α-helix	539-541	3
α-helix	548-558	11
α-helix	566-574	9
α-helix	582-587	6
α-helix	589-598	10
β-strand	607	1	5
β-strand	618-622	5	8
α-helix	624-628	5
α-helix	632-634	3
α-helix	637-657	21
β-strand	670-673	4	8
β-strand	680-685	6	8
β-strand	686-687	2	9
β-strand	690-694	5	9
α-helix	697-714	18
β-strand	722-723	2	8
α-helix	741-765	25

Chain C: 39 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	22-52	31
α-helix	59-79	21
α-helix	91-101	11
α-helix	104-107	4
α-helix	110-129	20
β-strand	132-133	2	10
β-strand	141-142	2	10
α-helix	144-148	5
α-helix	149-154	6
α-helix	158-168	11
α-helix	169-173	5
α-helix	174-193	20
α-helix	199-204	6
β-strand	209	1	11
β-strand	217	1	11
α-helix	219-231	13
α-helix	234-251	18
β-strand	260	1	12
α-helix	261	1
β-strand	262-263	2	13
α-helix	264-266	3
α-helix	276-281	6
α-helix	294-299	6
α-helix	306-316	11
α-helix	320-324	5
α-helix	325-329	5
β-strand	332	1	14
β-strand	347-352	6	14
β-strand	355-359	5	14
α-helix	366-383	18
α-helix	400-412	13
α-helix	415-420	6
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	13
α-helix	499-502	4
α-helix	504-507	4
α-helix	514-532	19
α-helix	548-558	11
α-helix	566-574	9
α-helix	582-587	6
α-helix	589-598	10
β-strand	607	1	12
β-strand	618-622	5	15
α-helix	624-627	4
α-helix	632-634	3
α-helix	637-657	21
β-strand	670-673	4	15
β-strand	680-685	6	15
β-strand	686-687	2	16
β-strand	690-694	5	16
α-helix	697-714	18
β-strand	722-723	2	15
α-helix	741-766	26

Chain D: 38 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	18-25	8
α-helix	38-53	16
α-helix	58-64	7
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-92	10
α-helix	100-107	8
α-helix	113-128	16
α-helix	131-141	11
α-helix	153-154	2
β-strand	155	1	17
β-strand	162	1	17
α-helix	164-168	5
α-helix	171-174	4
α-helix	175-180	6
α-helix	195-211	17
α-helix	215-226	12
α-helix	229-242	14
α-helix	250-255	6
α-helix	259-263	5
α-helix	266-278	13
α-helix	286-290	5
α-helix	299-348	50
α-helix	360-370	11
α-helix	397	1
α-helix	398-402	5
α-helix	403-409	7
α-helix	413-438	26
α-helix	441-445	5
α-helix	455-470	16
α-helix	471-474	4
α-helix	478-488	11
α-helix	492-505	14
α-helix	506-510	5
α-helix	511-521	11
α-helix	528-532	5
α-helix	533-537	5
α-helix	538-552	15
α-helix	582-590	9
α-helix	592-608	17

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

>8WBZ_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

>8WBZ_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
XF0	2-(4-bromanyl-3-methyl-phenoxy)-~{N}-propyl-ethanamide	C12 H16 Br N O2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

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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