6GH4: HLA-E*01:03

HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln. Determined by X-ray diffraction at 2.16 Å resolution. Released 8 Aug 2018.

Method: X-ray diffraction
Resolution: 2.16 Å
Organisms: Homo sapiens, Mycobacteriaceae
Chains: 12
Atoms: 13,596
Mol. weight: 178.63 kDa
Ligands: ZN
Released: 8 Aug 2018

Explore 6GH4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GH4 contains 57 α-helices and 120 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: 11 helices, 19 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	222	1	4
β-strand	229-230	2	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 H: 2 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	37-42	6	7
β-strand	45-46	2	7
α-helix	47	1
β-strand	51-52	2	6
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Chain C: 11 helices, 20 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	43	1	4
β-strand	46-47	2	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 D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	12
α-helix	5-6	2
β-strand	7-12	6	13
β-strand	22-31	10	13
β-strand	32	1	12
β-strand	37-42	6	14
β-strand	45-46	2	14
β-strand	51-52	2	13
α-helix	53-55	3
β-strand	56-57	2	13
β-strand	63-71	9	13
β-strand	79-84	6	14
β-strand	92-95	4	14

Chain E: 11 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
α-helix	176-179	4
β-strand	183	1	16
α-helix	184-185	2
β-strand	186-193	8	17
β-strand	198-208	11	17
β-strand	209	1	16
β-strand	214-219	6	18
β-strand	224-225	2	18
β-strand	229-230	2	17
α-helix	231-233	3
β-strand	234-235	2	17
β-strand	241-250	10	17
α-helix	254-256	3
β-strand	257-262	6	18
β-strand	270-272	3	18

Chain F: 3 helices, 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
α-helix	47	1
β-strand	51-52	2	20
α-helix	53-55	3
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: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	22
α-helix	20	1
β-strand	21-28	8	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	229-230	2	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	270-273	4	25

Chains P, Q, R and Y: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, C, E, G	protein	274	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	B, D, F, H	protein	100	Homo sapiens	P61769 (AlphaFold model)
Arg-gln-pro-ala-lys-ala-pro-leu-leu	P, Q, R, Y	protein	9	Mycobacteriaceae	P9WGR1 (AlphaFold model)

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

>6GH4_1 MHC class I antigen (chains A, C, E, G)
GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYW
DRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDG
KDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLL
HLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRW

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

>6GH4_2 Beta-2-microglobulin (chains B, D, F, H)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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

>6GH4_3 ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU (chains P, Q, R, Y)
RQPAKAPLL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding. Walters, L.C., Harlos, K., Brackenridge, S. et al. Nat Commun (2018) 9:3137-3137. DOI 10.1038/s41467-018-05459-z · PubMed

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

7P4B 1.72 Å, HLA-E*01:03 in complex with IL9
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
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

Browse structure collections

About this viewer

MolViewer shows 6GH4 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.