8KDI: 4F2 cell-surface antigen heavy chain

Structure of apo inward-open LAT1-CD98hc-Fab170 in nanodisc, consensus map. Determined by electron microscopy at 3.58 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 3.58 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 10,532
Mol. weight: 174.34 kDa
Ligands: NAG
Released: 12 Feb 2025

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

Secondary structure: helices and β-sheets

8KDI contains 69 α-helices and 67 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: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	166-172	7
α-helix	175-179	5
α-helix	180-206	27
α-helix	208-214	7
α-helix	218-221	4
β-strand	224-227	4	1
α-helix	241-254	14
β-strand	260-261	2	1
β-strand	265	1	2
β-strand	280	1	2
α-helix	282-284	3
α-helix	287-299	13
β-strand	305-307	3	1
α-helix	323-340	18
β-strand	344-347	4	1
α-helix	350-352	3
α-helix	356-370	15
β-strand	375-379	5	1
α-helix	385-394	10
β-strand	399-401	3	1
α-helix	404-406	3
α-helix	415-426	12
α-helix	441-443	3
α-helix	450-457	8
β-strand	465-467	3	1
α-helix	470-472	3
α-helix	487-489	3
α-helix	505-507	3
α-helix	509-513	5
α-helix	519-532	14
α-helix	534-538	5
β-strand	540-544	5	3
β-strand	545	1	4
β-strand	551-556	6	3
β-strand	562-567	6	3
β-strand	573-574	2	5
β-strand	581	1	4
β-strand	592-598	7	3
β-strand	608-610	3	3
α-helix	611-613	3
α-helix	616-617	2
β-strand	622-626	5	3

Chain B: 30 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	52-63	12
α-helix	67-69	3
α-helix	72-79	8
α-helix	82-109	28
α-helix	116-123	8
α-helix	126-135	10
α-helix	136-140	5
α-helix	141-157	17
α-helix	158-160	3
α-helix	165-167	3
α-helix	168-188	21
α-helix	190-221	32
α-helix	240-253	14
α-helix	257-260	4
α-helix	261-266	6
α-helix	273-297	25
α-helix	302-305	4
α-helix	311-319	9
α-helix	323-325	3
α-helix	327-344	18
α-helix	347-355	9
α-helix	361-364	4
β-strand	366	1	6
β-strand	367	1	7
β-strand	372	1	7
α-helix	374-386	13
α-helix	387-389	3
α-helix	393-421	29
α-helix	436-453	18
α-helix	455-466	12
α-helix	468-472	5
α-helix	473-477	5
α-helix	483-500	18
β-strand	503	1	6

Chain H: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
β-strand	9-12	4	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	45-51	7	15
β-strand	58-60	3	15
α-helix	62-64	3
β-strand	68-73	6	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-98	7	15
β-strand	109-110	2	15
α-helix	111-113	3
β-strand	114-118	5	15
α-helix	122-123	2
β-strand	124	1	16
β-strand	127-131	5	17
α-helix	137-139	3
β-strand	142-152	11	17
β-strand	153	1	16
β-strand	158	1	18
β-strand	161	1	18
β-strand	170-178	9	17
β-strand	181-191	11	17
α-helix	195-197	3
β-strand	201-206	6	18
β-strand	211-216	6	18

Chain L: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	30-31	2	10
β-strand	36-37	2	10
β-strand	39-44	6	9
β-strand	51-55	5	9
β-strand	59-60	2	9
α-helix	61	1
β-strand	68-73	6	8
β-strand	76-81	6	8
α-helix	86-88	3
β-strand	90-96	7	9
β-strand	99-100	2	5
β-strand	103-104	2	9
β-strand	108-113	6	9
β-strand	117	1	11
α-helix	118-119	2
β-strand	120-124	5	12
α-helix	125-127	3
α-helix	130-133	4
β-strand	135-145	11	12
β-strand	146	1	11
β-strand	150-156	7	13
β-strand	159-161	3	13
β-strand	165-169	5	12
α-helix	170-173	4
β-strand	179-188	10	12
α-helix	189-193	5
β-strand	197-204	8	13
α-helix	210	1
β-strand	211-216	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
4F2 cell-surface antigen heavy chain	A	protein	631	Homo sapiens	P08195 (AlphaFold model)
Large neutral amino acids transporter small subunit 1	B	protein	515	Homo sapiens	Q01650 (AlphaFold model)
Fab170 light chain	L	protein	220	Mus musculus
Fab170 heavy chain	H	protein	230	Mus musculus

Sequence of entity 1 (A), FASTA

>8KDI_1 4F2 cell-surface antigen heavy chain (chains A)
GSELQPPEASIAVVSIPRQLPGSHSEAGVQGLSAGDDSELGSHCVAQTGLELLASGDPLP
SASQNAEMIETGSDCVTQAGLQLLASSDPPALASKNAEVTGTMSQDTEVDMKEVELNELE
PEKQPMNAASGAAMSLAGAEKNGLVKIKVAEDEAEAAAAAKFTGLSKEELLKVAGSPGWV
RTRWALLLLFWLGWLGMLAGAVVIIVRAPRCRELPAQKWWHTGALYRIGDLQAFQGHGAG
NLAGLKGRLDYLSSLKVKGLVLGPIHKNQKDDVAQTDLLQIDPNFGSKEDFDSLLQSAKK
KSIRVILDLTPNYRGENSWFSTQVDTVATKVKDALEFWLQAGVDGFQVRDIENLKDASSF
LAEWQNITKGFSEDRLLIAGTNSSDLQQILSLLESNKDLLLTSSYLSDSGSTGEHTKSLV
TQYLNATGNRWCSWSLSQARLLTSFLPAQLLRLYQLMLFTLPGTPVFSYGDEIGLDAAAL
PGQPMEAPVMLWDESSFPDIPGAVSANMTVKGQSEDPGSLLSLFRRLSDQRSKERSLLHG
DFHAFSAGPGLFSYIRHWDQNERFLVVLNFGDVGLSAGLQASDLPASASLPAKADLLLST
QPGREEGSPLELERLKLEPHEGLLLRFPYAA

Sequence of entity 2 (B), FASTA

>8KDI_2 Large neutral amino acids transporter small subunit 1 (chains B)
MAGAGPKRRALAAPAAEEKEEAREKMLAAKSADGSAPAGEGEGVTLQRNITLLNGVAIIV
GTIIGSGIFVTPTGVLKEAGSPGLALVVWAACGVFSIVGALCYAELGTTISKSGGDYAYM
LEVYGSLPAFLKLWIELLIIRPSSQYIVALVFATYLLKPLFPTCPVPEEAAKLVACLCVL
LLTAVNCYSVKAATRVQDAFAAAKLLALALIILLGFVQIGKGDVSNLDPNFSFEGTKLDV
GNIVLALYSGLFAYGGWNYLNFVTEEMINPYRNLPLAIIISLPIVTLVYVLTNLAYFTTL
STEQMLSSEAVAVDFGNYHLGVMSWIIPVFVGLSCFGSVNGSLFTSSRLFFVGSREGHLP
SILSMIHPQLLTPVPSLVFTCVMTLLYAFSKDIFSVINFFSFFNWLCVALAIIGMIWLRH
RKPELERPIKVNLALPVFFILACLFLIAVSFWKTPVECGIGFTIILSGLPVYFFGVWWKN
KPKWLLQGIFSTTVLCQKLMQVVPQETDYKDDDDK

Sequence of entity 3 (L), FASTA

>8KDI_3 Fab170 light chain (chains L)
DIVLTQSPSSLAMSVGQKVTMNCKSSQSLLNNNNQKNYLAWYQQKPGQSPKLLVYFTSTR
ESGVPDRFIGSGSGTDFTLTISSVQAEDLALYYCQQHYTIPPTFGGGTKLEIKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 4 (H), FASTA

>8KDI_4 Fab170 heavy chain (chains H)
EVQLQQSGAELVKPGASVNLSCKASGYTFTNYWMHWVRLRPGQGLEWIGEIDPSDSYSYY
SQNFKGKATLTVDQSSNTAYLQLTSLTSEDSAVYYCARGRQTYYPWFPYWGQGTLVTVSA
AKTTPPSDYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCICT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structural basis of anticancer drug recognition and amino acid transport by LAT1. Lee, Y., Jin, C., Ohgaki, R. et al. Nat Commun (2025) 16:1635-1635. DOI 10.1038/s41467-025-56903-w · PubMed

Other PDB entries of the same protein (UniProt P08195 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8V 1.8 Å, Structure of the high affinity Anticalin P3D11 in complex with the human CD98 heavy…
2DH2 2.1 Å, Crystal Structure of human ED-4F2hc
8G0M 2.25 Å, Structure of complex between TV6.6 and CD98hc ECD
9KJU 2.7 Å, Local refinement of the y+LAT1-4F2hc bound with Arg
2DH3 2.8 Å, Crystal Structure of human ED-4F2hc
7DF1 2.81 Å, Crystal structure of human CD98 heavy chain extracellular domain in complex with S1-F4…
7CMI 2.9 Å, The LAT2-4F2hc complex in complex with leucine
7DSK 2.9 Å, Overall structure of the LAT1-4F2hc bound with JX-075
7DSL 2.9 Å, Overall structure of the LAT1-4F2hc bound with JX-078
8YLP 2.9 Å, Overall structure of the y+LAT1-4F2hc bound with Arg
7DSN 3.1 Å, Overall structure of the LAT1-4F2hc bound with JX-119
8X0W 3.1 Å, Overall structure of the LAT1-4F2hc bound with Leu

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