7DF1: Human CD98 heavy chain extracellular domain

Crystal structure of human CD98 heavy chain extracellular domain in complex with S1-F4 scFv. Determined by X-ray diffraction at 2.81 Å resolution. Released 7 Dec 2022.

Method: X-ray diffraction
Resolution: 2.81 Å
Organism: Homo sapiens
Chains: 12
Atoms: 19,740
Mol. weight: 298.27 kDa
Released: 7 Dec 2022

Explore 7DF1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DF1 contains 122 α-helices and 183 β-strands across 12 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, 19 β-strands

Element	Residues	Length	Sheet
α-helix	117-119	3
β-strand	123-126	4	1
α-helix	129-133	5
α-helix	140-143	4
α-helix	144-146	3
α-helix	147-152	6
β-strand	157-160	4	1
β-strand	164-166	3	2
β-strand	174-179	6	2
α-helix	181-183	3
α-helix	186-198	13
β-strand	202-206	5	1
α-helix	222-239	18
β-strand	243-246	4	1
α-helix	249-251	3
α-helix	255-269	15
β-strand	274-278	5	1
α-helix	284-291	8
β-strand	298-300	3	1
α-helix	311-324	14
β-strand	331-332	2	3
α-helix	340-342	3
α-helix	346-356	11
β-strand	362-363	2	3
β-strand	364-366	3	1
α-helix	369-371	3
α-helix	375-377	3
α-helix	386-388	3
α-helix	399-401	3
α-helix	404-406	3
α-helix	408-412	5
α-helix	418-431	14
α-helix	433-436	4
β-strand	440-442	3	4
β-strand	449-454	6	4
β-strand	461-467	7	4
β-strand	473-474	2	5
β-strand	491-497	7	4
β-strand	507-509	3	4
β-strand	514-515	2	5
β-strand	520-525	6	4

Chain B: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	117-119	3
β-strand	123-126	4	6
α-helix	129-133	5
α-helix	140-143	4
α-helix	144-146	3
α-helix	147-152	6
β-strand	157-160	4	6
β-strand	164-166	3	7
β-strand	174-179	6	7
α-helix	181-183	3
α-helix	186-198	13
β-strand	202-206	5	6
α-helix	222-239	18
β-strand	243-246	4	6
α-helix	249-251	3
α-helix	255-269	15
β-strand	274-278	5	6
α-helix	284-292	9
β-strand	298-300	3	6
α-helix	311-324	14
β-strand	331-332	2	8
α-helix	340-342	3
α-helix	346-348	3
α-helix	349-356	8
β-strand	362-363	2	8
β-strand	364-366	3	6
α-helix	369-371	3
α-helix	375-377	3
α-helix	386-388	3
α-helix	399-401	3
α-helix	404-406	3
α-helix	408-412	5
α-helix	418-431	14
α-helix	433-436	4
β-strand	440-442	3	9
β-strand	449-454	6	9
β-strand	461-467	7	9
β-strand	473-474	2	10
β-strand	491-497	7	9
β-strand	507-509	3	9
β-strand	514-515	2	10
α-helix	516	1
β-strand	520-525	6	9

Chain C: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	117-119	3
β-strand	123-126	4	11
α-helix	129-133	5
α-helix	140-144	5
α-helix	147-152	6
β-strand	157-160	4	11
β-strand	164-166	3	12
β-strand	174-179	6	12
α-helix	181-183	3
α-helix	186-198	13
β-strand	202-206	5	11
α-helix	222-239	18
β-strand	243-246	4	11
α-helix	249-251	3
α-helix	255-269	15
β-strand	274-278	5	11
α-helix	284-291	8
β-strand	298-300	3	11
α-helix	315-324	10
β-strand	331-332	2	13
α-helix	340-342	3
α-helix	346-348	3
α-helix	349-356	8
β-strand	362-363	2	13
β-strand	364-366	3	11
α-helix	369-371	3
α-helix	375-377	3
α-helix	386-388	3
α-helix	399-401	3
α-helix	404-406	3
α-helix	408-412	5
α-helix	418-431	14
α-helix	433-436	4
β-strand	440-442	3	14
β-strand	449-454	6	14
β-strand	461-467	7	14
β-strand	473-474	2	15
β-strand	491-497	7	14
β-strand	507-509	3	14
β-strand	514-515	2	15
β-strand	520-525	6	14

Chain D: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	117-119	3
β-strand	123-126	4	16
α-helix	129-133	5
α-helix	140-144	5
α-helix	147-152	6
β-strand	157-160	4	16
β-strand	164-166	3	17
β-strand	174-179	6	17
α-helix	181-183	3
α-helix	186-198	13
β-strand	202-206	5	16
α-helix	222-239	18
β-strand	243-246	4	16
α-helix	249-251	3
α-helix	255-269	15
β-strand	274-278	5	16
α-helix	284-291	8
β-strand	298-300	3	16
α-helix	315-324	10
β-strand	331-332	2	18
α-helix	340-342	3
α-helix	346-348	3
α-helix	349-356	8
β-strand	362-363	2	18
β-strand	364-366	3	16
α-helix	369-371	3
α-helix	375-377	3
α-helix	386-388	3
α-helix	399-401	3
α-helix	404-406	3
α-helix	408-412	5
α-helix	418-431	14
α-helix	433-436	4
β-strand	440-441	2	19
β-strand	449-454	6	19
β-strand	461-467	7	19
β-strand	473-474	2	20
β-strand	491-497	7	19
β-strand	507-509	3	19
β-strand	514-515	2	20
β-strand	520-525	6	19

Chains E, G and H: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	26
α-helix	7-9	3
β-strand	10-12	3	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	34-39	6	27
β-strand	45-51	7	27
β-strand	57-59	3	27
α-helix	61-63	3
β-strand	67-72	6	26
β-strand	77-82	6	26
α-helix	84-86	3
β-strand	88-95	8	27
α-helix	96	1
β-strand	98	1	28
β-strand	100c	1	28
β-strand	100h-103	4	27
β-strand	104	1	26
β-strand	107-111	5	27

Chain F: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	32
α-helix	7-9	3
β-strand	10-12	3	33
β-strand	18-25	8	32
α-helix	29-31	3
β-strand	34-39	6	33
β-strand	45-51	7	33
β-strand	57-59	3	33
α-helix	61-63	3
β-strand	67-72	6	32
β-strand	77-82	6	32
α-helix	84-86	3
β-strand	88-95	8	33
α-helix	96	1
β-strand	98	1	34
β-strand	100c	1	34
β-strand	100h-103	4	33
β-strand	107-111	5	33

Chains I and L: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	29
β-strand	10-12	3	30
β-strand	19-25	7	29
β-strand	27c-27d	2	31
β-strand	30-31	2	31
β-strand	33-38	6	30
β-strand	45-49	5	30
β-strand	53-54	2	30
α-helix	55	1
β-strand	62-67	6	29
β-strand	70-75	6	29
α-helix	80-82	3
β-strand	84-90	7	30
α-helix	96	1
β-strand	97-98	2	30
β-strand	102-105	4	30

Chains J and K: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-12	3	36
β-strand	19-25	7	35
β-strand	27c-27d	2	37
β-strand	30-31	2	37
β-strand	33-38	6	36
β-strand	45-49	5	36
β-strand	53-54	2	36
α-helix	55	1
β-strand	62-67	6	35
β-strand	70-75	6	35
α-helix	80-82	3
β-strand	85-90	6	36
α-helix	96	1
β-strand	97-98	2	36
β-strand	102-105	4	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
4F2 cell-surface antigen heavy chain	A, B, C, D	protein	420	Homo sapiens	P08195 (AlphaFold model)
S1-F4 vh	E, F, G, H	protein	140	Homo sapiens
IGL c2062_light_IGKV4-1_IGKJ5	I, J, K, L	protein	122	Homo sapiens	A0A5C2G3X0 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7DF1_1 4F2 cell-surface antigen heavy chain (chains A, B, C, D)
SELPAQKWWHTGALYRIGDLQAFQGHGAGNLAGLKGRLDYLSSLKVKGLVLGPIHKNQKD
DVAQTDLLQIDPNFGSKEDFDSLLQSAKKKSIRVILDLTPNYRGENSWFSTQVDTVATKV
KDALEFWLQAGVDGFQVRDIENLKDASSFLAEWQNITKGFSEDRLLIAGTNSSDLQQILS
LLESNKDLLLTSSYLSDSGSTGEHTKSLVTQYLNATGNRWCSWSLSQARLLTSFLPAQLL
RLYQLMLFTLPGTPVFSYGDEIGLDAAALPGQPMEAPVMLWDESSFPDIPGAVSANMTVK
GQSEDPGSLLSLFRRLSDQRSKERSLLHGDFHAFSAGPGLFSYIRHWDQNERFLVVLNFG
DVGLSAGLQASDLPASASLPAKADLLLSTQPGREEGSPLELERLKLEPHEGLLLRFPYAA

Sequence of entity 2 (E, F, G, H), FASTA

>7DF1_2 S1-F4 VH (chains E, F, G, H)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYYMHWVRQAPGQGLEWMGIINPSGGSTSY
AQKFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARGYYDILTGSRPIFFDIWGQGTM
VTVSSGGGGSGGGGSGGGGS

Sequence of entity 3 (I, J, K, L), FASTA

>7DF1_3 IGL c2062_light_IGKV4-1_IGKJ5 (chains I, J, K, L)
DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYNTPITFGQGTRLEIKAAAHHHH
HH

Primary citation

An anti-CD98 antibody displaying pH-dependent Fc-mediated tumour-specific activity against multiple cancers in CD98-humanized mice. Tian, X., Liu, X., Ding, J. et al. Nat Biomed Eng (2022). DOI 10.1038/s41551-022-00956-5 · 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
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
8A6L 3.18 Å, Human 4F2hc-LAT2 heterodimeric amino acid transporter in complex with anticalin D11vs

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