6JMQ: LAT1-CD98hc complex

LAT1-CD98hc complex bound to MEM-108 Fab. Determined by electron microscopy at 3.31 Å resolution. Released 19 Jun 2019.

Method: Electron microscopy
Resolution: 3.31 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 9,950
Mol. weight: 172.94 kDa
Ligands: NAG, CLR
Released: 19 Jun 2019

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

Secondary structure: helices and β-sheets

6JMQ contains 58 α-helices and 69 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: 29 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	52-63	12
β-strand	64	1	1
α-helix	66-69	4
α-helix	71-77	7
α-helix	82-109	28
α-helix	110-114	5
α-helix	119-125	7
α-helix	130-135	6
α-helix	136-140	5
α-helix	141-157	17
α-helix	165-167	3
α-helix	168-188	21
α-helix	190-200	11
α-helix	203-215	13
α-helix	240-243	4
α-helix	245-253	9
β-strand	254	1	1
α-helix	257-259	3
α-helix	261-264	4
α-helix	273-279	7
α-helix	283-291	9
α-helix	294-297	4
α-helix	311-316	6
α-helix	323-330	8
α-helix	334-351	18
α-helix	374-385	12
α-helix	386-389	4
α-helix	393-417	25
α-helix	434-453	20
α-helix	455-465	11
α-helix	468-477	10

Chain B: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	181-206	26
α-helix	208-214	7
β-strand	223	1	2
β-strand	224-226	3	3
α-helix	230-234	5
α-helix	242-247	6
α-helix	248-251	4
β-strand	256	1	2
β-strand	258-259	2	4
β-strand	265-267	3	5
β-strand	275-280	6	5
α-helix	287-298	12
β-strand	303-304	2	4
β-strand	306-307	2	6
α-helix	323-336	14
β-strand	345-346	2	6
α-helix	356-370	15
β-strand	376-379	4	6
α-helix	385-388	4
β-strand	399-401	3	6
α-helix	415-425	11
β-strand	433	1	7
α-helix	447-449	3
α-helix	450-459	10
β-strand	464	1	7
β-strand	465-467	3	3
α-helix	487-489	3
α-helix	509-513	5
α-helix	520-532	13
α-helix	535-538	4
β-strand	540-543	4	8
β-strand	545	1	9
β-strand	550-556	7	8
β-strand	562-568	7	8
α-helix	574-576	3
β-strand	579	1	9
β-strand	592-598	7	8
β-strand	601	1	10
β-strand	603	1	10
β-strand	608-610	3	8
α-helix	616-617	2
β-strand	621-626	6	8

Chain C: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	11
β-strand	11-12	2	12
β-strand	18-21	4	13
β-strand	24-25	2	11
α-helix	29-31	3
β-strand	33	1	14
β-strand	36-39	4	15
β-strand	46-49	4	15
α-helix	61-63	3
β-strand	67-72	6	13
β-strand	77-82	6	13
α-helix	87-89	3
β-strand	91-95	5	15
β-strand	98	1	14
β-strand	113-114	2	15
β-strand	115-116	2	12
β-strand	125-129	5	16
β-strand	140-150	11	16
β-strand	158-159	2	17
β-strand	169-170	2	16
α-helix	171-173	3
β-strand	174-176	3	16
β-strand	179-189	11	16
β-strand	199-201	3	17
β-strand	212-214	3	17
α-helix	215-218	4

Chain D: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	18
β-strand	10-13	4	19
β-strand	20-25	6	18
β-strand	30-31	2	20
β-strand	36-37	2	20
β-strand	40	1	21
β-strand	41-44	4	19
β-strand	51-55	5	19
β-strand	59-60	2	19
α-helix	61	1
β-strand	68-71	4	18
β-strand	76-81	6	18
β-strand	91-92	2	19
β-strand	95	1	21
β-strand	108-112	5	19
β-strand	120-124	5	22
α-helix	125-127	3
α-helix	128-133	6
β-strand	136-145	10	22
β-strand	152-156	5	23
β-strand	159-161	3	23
β-strand	165-169	5	22
α-helix	170-173	4
β-strand	179-187	9	22
α-helix	189-193	5
β-strand	197-202	6	23
α-helix	210	1
β-strand	211-216	6	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Large neutral amino acids transporter small subunit 1	A	protein	515	Homo sapiens	Q01650 (AlphaFold model)
4F2 cell-surface antigen heavy chain	B	protein	631	Homo sapiens	P08195 (AlphaFold model)
Antibody	C	protein	219	Mus musculus
Antibody	D	protein	219	Mus musculus

Sequence of entity 1 (A), FASTA

>6JMQ_1 Large neutral amino acids transporter small subunit 1 (chains A)
MAGAGPKRRALAAPAAEEKEEAREKMLAAKSADGSAPAGEGEGVTLQRNITLLNGVAIIV
GTIIGSGIFVTPTGVLKEAGSPGLALVVWAACGVFSIVGALCYAELGTTISKSGGDYAYM
LEVYGSLPAFLKLWIELLIIRPSSQYIVALVFATYLLKPLFPTCPVPEEAAKLVACLCVL
LLTAVNCYSVKAATRVQDAFAAAKLLALALIILLGFVQIGKGDVSNLDPNFSFEGTKLDV
GNIVLALYSGLFAYGGWNYLNFVTEEMINPYRNLPLAIIISLPIVTLVYVLTNLAYFTTL
STEQMLSSEAVAVDFGNYHLGVMSWIIPVFVGLSCFGSVNGSLFTSSRLFFVGSREGHLP
SILSMIHPQLLTPVPSLVFTCVMTLLYAFSKDIFSVINFFSFFNWLCVALAIIGMIWLRH
RKPELERPIKVNLALPVFFILACLFLIAVSFWKTPVECGIGFTIILSGLPVYFFGVWWKN
KPKWLLQGIFSTTVLCQKLMQVVPQETDYKDDDDK

Sequence of entity 2 (B), FASTA

>6JMQ_2 4F2 cell-surface antigen heavy chain (chains B)
GSELQPPEASIAVVSIPRQLPGSHSEAGVQGLSAGDDSELGSHCVAQTGLELLASGDPLP
SASQNAEMIETGSDCVTQAGLQLLASSDPPALASKNAEVTGTMSQDTEVDMKEVELNELE
PEKQPMNAASGAAMSLAGAEKNGLVKIKVAEDEAEAAAAAKFTGLSKEELLKVAGSPGWV
RTRWALLLLFWLGWLGMLAGAVVIIVRAPRCRELPAQKWWHTGALYRIGDLQAFQGHGAG
NLAGLKGRLDYLSSLKVKGLVLGPIHKNQKDDVAQTDLLQIDPNFGSKEDFDSLLQSAKK
KSIRVILDLTPNYRGENSWFSTQVDTVATKVKDALEFWLQAGVDGFQVRDIENLKDASSF
LAEWQNITKGFSEDRLLIAGTNSSDLQQILSLLESNKDLLLTSSYLSDSGSTGEHTKSLV
TQYLNATGNRWCSWSLSQARLLTSFLPAQLLRLYQLMLFTLPGTPVFSYGDEIGLDAAAL
PGQPMEAPVMLWDESSFPDIPGAVSANMTVKGQSEDPGSLLSLFRRLSDQRSKERSLLHG
DFHAFSAGPGLFSYIRHWDQNERFLVVLNFGDVGLSAGLQASDLPASASLPAKADLLLST
QPGREEGSPLELERLKLEPHEGLLLRFPYAA

Sequence of entity 3 (C), FASTA

>6JMQ_3 Antibody (chains C)
QVQLKESGPGLVAPSQSLSITCTVSGFPLTXXXXXWVRQPPGKGLEWLGXXXXXXXXXXX
XXXXXRLSISKDNSKSQVFLKMNSLQTDDTARYYCARXXXXXXXXXXWGQGTSVTVSSAK
TTPPSVYPLAPGSXXXXXSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD

Sequence of entity 4 (D), FASTA

>6JMQ_4 Antibody (chains D)
DIVMSQSPSSLVVSVGEKVTMSCXXXXXXXXXXXXXXXXXWYQQKPGQSPKLLIYXXXXX
XXGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCXXXXXXXXXFGGGTKLEIKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
CLR	Cholesterol	C27 H46 O	5

Primary citation

Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc. Lee, Y., Wiriyasermkul, P., Jin, C. et al. Nat Struct Mol Biol (2019) 26:510-517. DOI 10.1038/s41594-019-0237-7 · PubMed

Other PDB entries of the same protein (UniProt Q01650 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
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
8IDA 3.2 Å, Overall structure of the LAT1-4F2hc bound with tyrosine
6IRS 3.3 Å, human LAT1-4F2hc complex incubated with JPH203
8XPU 3.3 Å, Overall structure of the LAT1-4F2hc bound with JPH203
7DSQ 3.4 Å, Overall structure of the LAT1-4F2hc bound with 3,5-diiodo-L-tyrosine
6IRT 3.5 Å, human LAT1-4F2hc complex bound with BCH
8J8L 3.56 Å, Overall structure of the LAT1-4F2hc bound with L-dopa
8J8M 3.58 Å, Overall structure of the LAT1-4F2hc bound with tryptophan
8KDI 3.58 Å, Structure of apo inward-open LAT1-CD98hc-Fab170 in nanodisc, consensus map

Browse structure collections

About this viewer

MolViewer shows 6JMQ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.