4H1L: PDB entry 4H1L

TCR interaction with peptide mimics of nickel offers structural insights in nickel contact allergy. Determined by X-ray diffraction at 3.3 Å resolution. Released 14 Nov 2012.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 10
Atoms: 9,630
Mol. weight: 138.35 kDa
Released: 14 Nov 2012

Explore 4H1L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4H1L contains 29 α-helices and 124 β-strands across 10 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: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-51	6
β-strand	53	1	2
α-helix	56-75	20
α-helix	80-84	5
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	121-123	3	5
β-strand	126-128	3	5
β-strand	133-134	2	4
α-helix	135-137	3
β-strand	138-139	2	4
β-strand	145-147	3	4
β-strand	149-153	5	4
β-strand	160-165	6	5
β-strand	174-179	6	5

Chain B: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	36-41	6	1
β-strand	47-49	3	1
α-helix	55-61	7
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	6
β-strand	98-103	6	7
β-strand	115-122	8	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-137	2	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-161	7	7
β-strand	170-177	8	8
β-strand	180-189	10	8

Chains C and F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	0	1	2
α-helix	6-10	5

Chain D: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	9
β-strand	19-26	8	9
β-strand	29-35	7	9
β-strand	40-43	4	9
α-helix	48-51	4
β-strand	53	1	10
α-helix	56-75	20
α-helix	80-84	5
β-strand	85	1	11
α-helix	86-87	2
β-strand	88-93	6	12
β-strand	103-112	10	12
β-strand	113	1	11
β-strand	121-123	3	13
β-strand	126-128	3	13
β-strand	133-134	2	12
α-helix	135-137	3
β-strand	138-139	2	12
β-strand	145-147	3	12
β-strand	149-153	5	12
β-strand	160-165	6	13
β-strand	174-179	6	13

Chain E: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	9
β-strand	23-32	10	9
β-strand	36-41	6	9
β-strand	47-49	3	9
α-helix	55-61	7
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-87	7
β-strand	95	1	14
β-strand	98-103	6	15
β-strand	115-122	8	15
β-strand	123	1	14
β-strand	128-133	6	16
β-strand	136-137	2	16
β-strand	142-144	3	15
β-strand	148-149	2	15
β-strand	155-161	7	15
β-strand	170-177	8	16
β-strand	180-189	10	16

Chain G: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	17
β-strand	9-13	5	18
β-strand	18	1	19
β-strand	23-24	2	17
β-strand	31-37	7	18
α-helix	43	1
β-strand	44-49	6	18
β-strand	55-57	3	17
β-strand	63-67	5	17
β-strand	72-76	5	17
β-strand	77	1	19
α-helix	82-84	3
β-strand	87-93	7	18
β-strand	101-103	3	18
β-strand	107-112	6	18

Chains H and J: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	20
β-strand	8-10	3	21
β-strand	18-19	2	22
β-strand	20-23	4	20
β-strand	29-35	7	21
β-strand	41-47	7	21
β-strand	54-55	2	21
β-strand	62-64	3	22
β-strand	68	1	20
β-strand	71	1	20
β-strand	74-76	3	22
β-strand	86-92	7	21
β-strand	94	1	23
β-strand	98	1	23
α-helix	99-101	3
β-strand	102-103	2	21
β-strand	107-110	4	21

Chain I: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	24
β-strand	9-13	5	25
β-strand	18	1	26
β-strand	23-24	2	24
β-strand	31-37	7	25
α-helix	43	1
β-strand	44-49	6	25
β-strand	55-57	3	24
β-strand	63-67	5	24
α-helix	68-70	3
β-strand	72-76	5	24
β-strand	77	1	26
α-helix	82-84	3
β-strand	87-93	7	25
β-strand	101-103	3	25
β-strand	107-112	6	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, D	protein	178	Homo sapiens	P01903 (AlphaFold model)
MHC class II antigen	B, E	protein	187	Homo sapiens	P79483 (AlphaFold model)
mimotope peptide	C, F	protein	13	Escherichia coli
Ani2.3 TCR A chain	G, I	protein	113	Escherichia coli	L7MTK9 (AlphaFold model)
Ani2.3 TCR B chain	H, J	protein	111	Escherichia coli	L7MTL0 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4H1L_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, D)
EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALAN
IAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWL
RNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF

Sequence of entity 2 (B, E), FASTA

>4H1L_2 MHC class II antigen (chains B, E)
RPRFLELLKSECHFFNGTERVRFLERYFHNQEEFVRFDSDVGEYRAVTELGRPVAESWNS
QKDLLEQKRGQVDNYCRHNYGVVESFTVQRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFY
PGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSP
LTVEWRA

Sequence of entity 3 (C, F), FASTA

>4H1L_3 mimotope peptide (chains C, F)
QHIRCNIPKRISA

Sequence of entity 4 (G, I), FASTA

>4H1L_4 Ani2.3 TCR A chain (chains G, I)
QSVTQPDIHITVSEGASLELRCNYSYGATPYLFWYVQSPGQGLQLLLKYFSGDTLVQGIK
GFEAEFKRSQSSFNLRKPSVHWSDAAEYFCAVGASGNTGKLIFGQGTTLQVKP

Sequence of entity 5 (H, J), FASTA

>4H1L_5 Ani2.3 TCR B chain (chains H, J)
GITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDIAE
GYSVSREKKESFPLTVTSAQKNPTAFYLCASSLRDGYTGELFFGEGSRLTV

Primary citation

T-cell receptor (TCR) interaction with peptides that mimic nickel offers insight into nickel contact allergy. Yin, L., Crawford, F., Marrack, P. et al. Proc Natl Acad Sci U S A (2012) 109:18517-18522. DOI 10.1073/pnas.1215928109 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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