5HGB: HLA*A2402

HLA*A2402 complexed with HIV nef138 8mer epitope. Determined by X-ray diffraction at 2.4 Å resolution. Released 8 Jun 2016.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Human immunodeficiency virus type 1
Chains: 12
Atoms: 13,137
Mol. weight: 178.41 kDa
Released: 8 Jun 2016

Explore 5HGB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HGB contains 53 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: 10 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	50-52	3
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	138-150	13
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
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	213-219	7	4
β-strand	223	1	4
β-strand	228-230	3	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-263	7	4
β-strand	270-272	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	45	1	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chains C, F, I and L: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Chain D: 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	46-47	2	8
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	122-126	5	8
β-strand	133-135	3	8
α-helix	140-150	11
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	188-193	6	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	213-219	7	11
β-strand	223	1	11
β-strand	228-230	3	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	257-263	7	11
β-strand	270-273	4	11

Chains E and K: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Chain G: 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	57-85	29
β-strand	94-103	10	15
β-strand	109-118	10	15
β-strand	122-126	5	15
β-strand	133-135	3	15
α-helix	140-150	11
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	16
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	222-223	2	18
β-strand	228-230	3	17
β-strand	234-235	2	17
β-strand	241-250	10	17
β-strand	257-262	6	18
β-strand	270-273	4	18

Chain H: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	19
α-helix	4-5	2
β-strand	6-11	6	20
β-strand	21-30	10	20
β-strand	31	1	19
β-strand	36-41	6	21
β-strand	45	1	21
β-strand	50-51	2	20
α-helix	52-54	3
β-strand	55-56	2	20
β-strand	62-70	9	20
β-strand	78-83	6	21
α-helix	90	1
β-strand	91-94	4	21

Chain J: 9 helices, 19 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	50-53	4
α-helix	57-85	29
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	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	23
β-strand	186-195	10	24
β-strand	198-208	11	24
β-strand	209	1	23
β-strand	214-219	6	25
β-strand	222-223	2	25
β-strand	228-230	3	24
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-24 alpha chain	A, D, G, J	protein	275	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, E, H, K	protein	100	Homo sapiens	P61769 (AlphaFold model)
Protein Nef	C, F, I, L	protein	8	Human immunodeficiency virus type 1	P04601 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>5HGB_1 HLA class I histocompatibility antigen, A-24 alpha chain (chains A, D, G, J)
MGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETL
QRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 2 (B, E, H, K), FASTA

>5HGB_2 Beta-2-microglobulin (chains B, E, H, K)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F, I, L), FASTA

>5HGB_3 Protein Nef (chains C, F, I, L)
RYPLTFGW

Primary citation

Effects of a Single Escape Mutation on T Cell and HIV-1 Co-adaptation. Sun, X., Shi, Y., Akahoshi, T. et al. Cell Rep (2016) 15:2279-2291. DOI 10.1016/j.celrep.2016.05.017 · PubMed

Other PDB entries of the same protein (UniProt P04439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
3D25 1.3 Å, Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC…
3MRG 1.3 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081…
6JOZ 1.35 Å, Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.
5C0G 1.37 Å, HLA-A02 carrying YLGGPDFPTI
5N1Y 1.39 Å, HLA-A02 carrying MVWGPDPLYV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
3MRB 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503…
3MRK 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with AFP137 nonapeptide
6J2A 1.4 Å, The structure of HLA-A*3003/NP44
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide

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