8IDA: Overall structure of the LAT1-4F2hc

Overall structure of the LAT1-4F2hc bound with tyrosine. Determined by electron microscopy at 3.2 Å resolution. Released 10 Jul 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,372
Mol. weight: 129.23 kDa
Ligands: TYR
Released: 10 Jul 2024

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

Secondary structure: helices and β-sheets

8IDA contains 47 α-helices and 24 β-strands across 2 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: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	167-174	8
α-helix	180-206	27
α-helix	209-211	3
β-strand	225-228	4	1
α-helix	231-234	4
α-helix	242-244	3
α-helix	245-255	11
β-strand	261-262	2	1
α-helix	263-264	2
β-strand	266	1	2
α-helix	273-275	3
β-strand	281	1	2
α-helix	282	1
α-helix	288-300	13
β-strand	306-308	3	1
α-helix	324-341	18
β-strand	345-348	4	1
α-helix	351-353	3
α-helix	357-369	13
β-strand	376-380	5	1
α-helix	386-392	7
β-strand	400-402	3	1
α-helix	413-427	15
β-strand	432-434	3	3
α-helix	442-444	3
α-helix	451-458	8
β-strand	463-465	3	3
β-strand	466-468	3	1
α-helix	488-490	3
α-helix	510-515	6
α-helix	520-531	12
α-helix	535-539	5
β-strand	541-545	5	4
β-strand	551-557	7	4
β-strand	563-569	7	4
β-strand	575-576	2	5
α-helix	586-588	3
β-strand	593-594	2	6
β-strand	599	1	4
β-strand	610-611	2	6
β-strand	616-617	2	5
β-strand	621-627	7	4

Chain B: 25 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	7
α-helix	52-63	12
α-helix	67-79	13
α-helix	82-109	28
α-helix	118-123	6
α-helix	126-135	10
α-helix	136-140	5
α-helix	141-156	16
α-helix	165-167	3
α-helix	168-188	21
α-helix	191-220	30
α-helix	240-253	14
α-helix	261-263	3
β-strand	267	1	7
α-helix	270-297	28
α-helix	302-306	5
α-helix	311-319	9
α-helix	326-355	30
β-strand	365-366	2	8
α-helix	374-385	12
α-helix	386-389	4
α-helix	393-399	7
α-helix	403-421	19
α-helix	435-453	19
α-helix	455-466	12
α-helix	469-471	3
α-helix	472-477	6
α-helix	483-500	18
β-strand	503-504	2	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
4F2 cell-surface antigen heavy chain	A	protein	647	Homo sapiens	P08195 (AlphaFold model)
Large neutral amino acids transporter small subunit 1	B	protein	527	Homo sapiens	Q01650 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8IDA_1 4F2 cell-surface antigen heavy chain (chains A)
MAHHHHHHHHHHSGRELQPPEASIAVVSIPRQLPGSHSEAGVQGLSAGDDSETGSDCVTQ
AGLQLLASSDPPALASKNAEVTVETGFHHVSQADIEFLTSIDPTASASGSAGITGTMSQD
TEVDMKEVELNELEPEKQPMNAASGAAMSLAGAEKNGLVKIKVAEDEAEAAAAAKFTGLS
KEELLKVAGSPGWVRTRWALLLLFWLGWLGMLAGAVVIIVRAPRCRELPAQKWWHTGALY
RIGDLQAFQGHGAGNLAGLKGRLDYLSSLKVKGLVLGPIHKNQKDDVAQTDLLQIDPNFG
SKEDFDSLLQSAKKKSIRVILDLTPNYRGENSWFSTQVDTVATKVKDALEFWLQAGVDGF
QVRDIENLKDASSFLAEWQNITKGFSEDRLLIAGTNSSDLQQILSLLESNKDLLLTSSYL
SDSGSTGEHTKSLVTQYLNATGNRWCSWSLSQARLLTSFLPAQLLRLYQLMLFTLPGTPV
FSYGDEIGLDAAALPGQPMEAPVMLWDESSFPDIPGAVSANMTVKGQSEDPGSLLSLFRR
LSDQRSKERSLLHGDFHAFSAGPGLFSYIRHWDQNERFLVVLNFGDVGLSAGLQASDLPA
SASLPAKADLLLSTQPGREEGSPLELERLKLEPHEGLLLRFPYAALE

Sequence of entity 2 (B), FASTA

>8IDA_2 Large neutral amino acids transporter small subunit 1 (chains B)
MADYKDDDDKSGPDEVDASGRAGAGPKRRALAAPAAEEKEEAREKMLAAKSADGSAPAGE
GEGVTLQRNITLLNGVAIIVGTIIGSGIFVTPTGVLKEAGSPGLALVVWAACGVFSIVGA
LCYAELGTTISKSGGDYAYMLEVYGSLPAFLKLWIELLIIRPSSQYIVALVFATYLLKPL
FPTCPVPEEAAKLVACLCVLLLTAVNCYSVKAATRVQDAFAAAKLLALALIILLGFVQIG
KGDVSNLDPNFSFEGTKLDVGNIVLALYSGLFAYGGWNYLNFVTEEMINPYRNLPLAIII
SLPIVTLVYVLTNLAYFTTLSTEQMLSSEAVAVDFGNYHLGVMSWIIPVFVGLSCFGSVN
GSLFTSSRLFFVGSREGHLPSILSMIHPQLLTPVPSLVFTCVMTLLYAFSKDIFSVINFF
SFFNWLCVALAIIGMIWLRHRKPELERPIKVNLALPVFFILACLFLIAVSFWKTPVECGI
GFTIILSGLPVYFFGVWWKNKPKWLLQGIFSTTVLCQKLMQVVPQET

Ligands and cofactors

ID	Name	Formula	Copies
TYR	Tyrosine	C9 H11 N O3	1

Primary citation

Structural insights into the substrate transport mechanism of the amino acid transporter complex. Yang, H., Shi, T., Dong, J. et al. J Biol Chem (2025) 301:110569-110569. DOI 10.1016/j.jbc.2025.110569 · 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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