7P4B: HLA-E*01:03

HLA-E*01:03 in complex with IL9. Determined by X-ray diffraction at 1.72 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 1.72 Å
Organisms: Homo sapiens, Mycobacterium tuberculosis H37Rv
Chains: 12
Atoms: 13,836
Mol. weight: 182.35 kDa
Ligands: PO4, ZN
Released: 27 Jul 2022

Explore 7P4B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P4B contains 54 α-helices and 119 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: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	227-230	4	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chains B and D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	36-42	7	7
β-strand	45-46	2	7
α-helix	47	1
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-85	7	7
β-strand	92-95	4	7

Chain C: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	45-47	3	8
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222	1	11
β-strand	229-230	2	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Chain E: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	15
α-helix	20	1
β-strand	21-28	8	15
β-strand	31-37	7	15
β-strand	46-47	2	15
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	15
β-strand	109-118	10	15
β-strand	121-126	6	15
β-strand	133-135	3	15
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
β-strand	183	1	16
β-strand	186	1	17
β-strand	189	1	17
β-strand	201-208	8	17
β-strand	209	1	16
β-strand	215-219	5	18
β-strand	229-230	2	17
α-helix	231-233	3
β-strand	234-235	2	17
β-strand	241-247	7	17
β-strand	257-261	5	18
β-strand	270-272	3	18

Chain F: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	19
α-helix	5-6	2
β-strand	7-12	6	20
β-strand	22-31	10	20
β-strand	32	1	19
β-strand	37-42	6	21
β-strand	45-46	2	21
β-strand	51-52	2	20
β-strand	56-57	2	20
β-strand	63-71	9	20
β-strand	79-84	6	21
β-strand	92-95	4	21

Chain G: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	22
β-strand	18-28	11	22
β-strand	31-37	7	22
β-strand	46-47	2	22
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	22
β-strand	109-118	10	22
β-strand	121-126	6	22
β-strand	133-135	3	22
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	23
α-helix	184-185	2
β-strand	186-193	8	24
β-strand	198-208	11	24
β-strand	209	1	23
β-strand	214-219	6	25
β-strand	222	1	25
β-strand	228-230	3	24
α-helix	231-233	3
β-strand	234-235	2	24
β-strand	241-250	10	24
α-helix	254-256	3
β-strand	257-262	6	25
β-strand	270-272	3	25

Chain H: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	26
α-helix	5-6	2
β-strand	7-12	6	27
β-strand	22-31	10	27
β-strand	32	1	26
β-strand	37-42	6	28
β-strand	45-46	2	28
α-helix	47	1
β-strand	51-52	2	27
α-helix	53-55	3
β-strand	56-57	2	27
β-strand	63-71	9	27
β-strand	79-84	6	28
β-strand	92-95	4	28

Chains P and Z: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
α-helix	6-8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	A, C, E, G	protein	277	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	B, D, F, H	protein	100	Homo sapiens	P61769 (AlphaFold model)
ESAT-6-like protein EsxH	P, Q, R, Z	protein	9	Mycobacterium tuberculosis H37Rv	P9WNK3 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>7P4B_1 HLA class I histocompatibility antigen, alpha chain E (chains A, C, E, G)
GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYW
DRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDG
KDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLL
HLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKPP

Sequence of entity 2 (B, D, F, H), FASTA

>7P4B_2 Beta-2-microglobulin (chains B, D, F, H)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (P, Q, R, Z), FASTA

>7P4B_3 ESAT-6-like protein EsxH (chains P, Q, R, Z)
IMYNYPAML

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
ZN	Zinc ion	Zn	2

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

Primary and secondary functions of HLA-E are determined by stability and conformation of the peptide-bound complexes. Walters, L.C., Rozbesky, D., Harlos, K. et al. Cell Rep (2022) 39:110959-110959. DOI 10.1016/j.celrep.2022.110959 · PubMed

Other PDB entries of the same protein (UniProt P13747 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BH8 1.8 Å, 3H4-Fab HLA-E-VL9 co-complex
7P49 2.05 Å, HLA-E*01:03 in complex with Mtb14
6GH1 2.1 Å, HLA-E*01:03 in complex with Mtb44
9NW7 2.1 Å, CA117v2v8 Fab bound to HLA-E-VL9
6GH4 2.16 Å, HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln.
6ZKX 2.17 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG)
8RLT 2.25 Å, TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index peptide
6ZKW 2.26 Å, Crystal structure of InhA:01 TCR in complex with HLA-E bound to InhA (53-61)
6ZKZ 2.3 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (F116C) bound to InhA (53-61 H4C)
9NW8 2.3 Å, CA117v2v8 Fab bound to HLA-E-Mtb44
9NW9 2.3 Å, CA117v2v8 Fab bound to HLA-E-RL9HIV
8QFY 2.33 Å, Crystal structure of high affinity TCR in complex with pHLA harbouring bacterial peptide

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