1JL4: PDB entry 1JL4

Crystal structure of the human CD4 N-terminal two domain fragment complexed to a class II MHC molecule. Determined by X-ray diffraction at 4.3 Å resolution. Released 19 Sept 2001.

Method: X-ray diffraction
Resolution: 4.3 Å
Organisms: Mus musculus, Gallus gallus, Homo sapiens
Chains: 4
Atoms: 4,474
Mol. weight: 63.74 kDa
Released: 19 Sept 2001

Explore 1JL4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1JL4 contains 21 α-helices and 55 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: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-50	5
β-strand	53-54	2	2
α-helix	56-77	22
α-helix	81-84	4
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	118-123	6	4
β-strand	126-127	2	4
β-strand	132-134	3	3
α-helix	137	1
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
β-strand	174-178	5	4

Chain B: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
α-helix	20-22	3
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-64	10
α-helix	68-72	5
α-helix	74	1
α-helix	75-80	6
α-helix	81-82	2
α-helix	83-86	5
α-helix	90-92	3
β-strand	95	1	5
α-helix	96-97	2
β-strand	98-103	6	6
α-helix	106-107	2
β-strand	113-122	10	6
β-strand	123	1	5
β-strand	128-133	6	7
β-strand	136-138	3	7
β-strand	142-144	3	6
β-strand	145	1	8
α-helix	146-147	2
β-strand	148-149	2	6
β-strand	155-163	9	6
β-strand	170-176	7	7
β-strand	184-189	6	7

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	133-134	2	2
α-helix	139-141	3

Chain D: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	12-14	3	9
β-strand	17	1	10
β-strand	26-30	5	8
β-strand	35-40	6	8
β-strand	43-45	3	8
β-strand	55-56	2	9
α-helix	59-64	6
β-strand	66	1	10
β-strand	69-71	3	9
α-helix	76-78	3
β-strand	80-86	7	8
β-strand	89-98	10	8
β-strand	99-102	4	11
β-strand	108-109	2	12
α-helix	112-113	2
β-strand	114-119	6	11
β-strand	127-129	3	13
β-strand	131	1	14
β-strand	139-140	2	13
β-strand	143-146	4	11
α-helix	151-153	3
β-strand	155-156	2	15
β-strand	158	1	14
β-strand	159-163	5	13
β-strand	166-170	5	13
β-strand	173-174	2	15
β-strand	176-177	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen, a-K alpha chain	A	protein	178	Mus musculus	P01910 (AlphaFold model)
H-2 class II histocompatibility antigen, a-K beta chain	B	protein	185	Mus musculus	P06343 (AlphaFold model)
Ovotransferrin	C	protein	16	Gallus gallus	P02789 (AlphaFold model)
T-cell surface glycoprotein CD4	D	protein	178	Homo sapiens	P01730 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1JL4_1 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K ALPHA CHAIN (chains A)
HVGSYGITVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFAQLRRFEPQGGLQNI
ATGKHNLEILTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLR
NSKSVTDGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPE

Sequence of entity 2 (B), FASTA

>1JL4_2 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K BETA CHAIN (chains B)
GSFVHQFQPFCYFTNGTQRIRLVIRYIYNREEYVRFDSDVGEYRAVTELGRPDAEYWNKQ
YLERTRAELDTVCRHNYEKTETPTSLRRLEQPSVVISLSRTEALNHHNTLVCSVTDFYPA
KIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLTSPIT
VEWRA

Sequence of entity 3 (C), FASTA

>1JL4_3 OVOTRANSFERRIN (chains C)
GNSHRGAIEWEGIESG

Sequence of entity 4 (D), FASTA

>1JL4_4 T-CELL SURFACE GLYCOPROTEIN CD4 (chains D)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLA

Primary citation

Crystal structure of the human CD4 N-terminal two-domain fragment complexed to a class II MHC molecule. Wang, J.H., Meijers, R., Xiong, Y. et al. Proc Natl Acad Sci U S A (2001) 98:10799-10804. DOI 10.1073/pnas.191124098 · PubMed

Other PDB entries of the same protein (UniProt P01910 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1IAK 1.9 Å, Histocompatibility antigen I-ak
9L1L 3.09 Å, Structure of anti-HEL AiTab
1D9K 3.2 Å, Crystal structure of complex between D10 TCR and pmhc I-ak/ca

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