4MJI: PDB entry 4MJI

T cell response to a HIV reverse transcriptase epitope presented by the protective allele HLA-B*51:01. Determined by X-ray diffraction at 2.99 Å resolution. Released 28 May 2014.

Method: X-ray diffraction
Resolution: 2.99 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 10
Atoms: 13,067
Mol. weight: 186.35 kDa
Released: 28 May 2014

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

Secondary structure: helices and β-sheets

4MJI contains 42 α-helices and 147 β-strands across 9 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: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
β-strand	18-28	11	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	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
β-strand	188-193	6	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6	1	6
β-strand	9-11	3	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	1	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

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Chain D: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	8
α-helix	18-19	2
β-strand	20-24	5	9
β-strand	32-38	7	8
β-strand	48-50	3	8
β-strand	55-58	4	9
β-strand	61-66	6	9
β-strand	71-76	6	9
α-helix	81-83	3
β-strand	85-92	8	8
β-strand	99-101	3	8
β-strand	105-110	6	8
β-strand	119-125	7	10
β-strand	132-137	6	10
β-strand	150	1	11
β-strand	153	1	11
β-strand	154-155	2	10
α-helix	156-158	3
β-strand	160-163	4	12
α-helix	164-166	3
β-strand	168-171	4	12
β-strand	172-177	6	10
α-helix	184-187	4

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	13
β-strand	13-17	5	14
β-strand	22-27	6	13
β-strand	34-40	7	14
β-strand	47-53	7	14
β-strand	56-59	4	14
β-strand	68-71	4	13
β-strand	78-82	5	13
α-helix	87-89	3
β-strand	91-97	7	14
β-strand	106-107	2	14
β-strand	111-116	6	14
β-strand	123	1	15
α-helix	124-125	2
β-strand	126-131	6	10
α-helix	132-133	2
α-helix	134-139	6
β-strand	142-152	11	10
β-strand	153	1	15
β-strand	157-163	7	16
β-strand	166-167	2	16
β-strand	172-174	3	10
β-strand	179-180	2	10
β-strand	190-199	10	10
α-helix	200-204	5
β-strand	209-216	8	16
β-strand	219	1	17
β-strand	233	1	17
β-strand	236-242	7	16

Chain F: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	18
β-strand	18-28	11	18
β-strand	31-37	7	18
β-strand	46-47	2	18
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	18
β-strand	109-118	10	18
β-strand	121-126	6	18
β-strand	133-135	3	18
α-helix	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	19
β-strand	186-193	8	20
β-strand	198-208	11	20
β-strand	209	1	19
β-strand	214-219	6	21
β-strand	228-230	3	20
β-strand	234-235	2	20
β-strand	241-250	10	20
β-strand	257-262	6	21
β-strand	270-272	3	21

Chain G: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	22
β-strand	6	1	23
β-strand	9-11	3	23
β-strand	21-30	10	23
β-strand	31	1	22
β-strand	36-41	6	24
β-strand	45	1	24
β-strand	50	1	23
α-helix	52-54	3
β-strand	55-56	2	23
β-strand	62-70	9	23
β-strand	78-83	6	24
β-strand	91-94	4	24
α-helix	95-96	2

Chain I: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	25
α-helix	18	1
β-strand	19-24	6	26
β-strand	30-38	9	27
β-strand	45	1	27
β-strand	48-50	3	27
β-strand	55-58	4	26
β-strand	61-66	6	26
β-strand	71-76	6	26
α-helix	81-83	3
β-strand	86-93	8	27
β-strand	99-101	3	27
β-strand	106	1	27
β-strand	107-110	4	25
β-strand	119-121	3	28
β-strand	125	1	29
β-strand	133-137	5	28
α-helix	143-145	3
β-strand	154-155	2	28
α-helix	156-158	3
β-strand	160-163	4	30
α-helix	164-166	3
β-strand	168-171	4	30
β-strand	172-176	5	28
α-helix	184-187	4

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, B-51 alpha chain	A, F	protein	276	Homo sapiens	P01889 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	99	Homo sapiens	P61769 (AlphaFold model)
HIV Reverse Transcriptase peptide Marker	C, H	protein	8	Human immunodeficiency virus 1	R4WL38
T-Cell Receptor Chain alpha	D, I	protein	195	Homo sapiens	K7N5M3 (AlphaFold model)
T-cell Receptor Beta chain	E, J	protein	242	Homo sapiens	P01850

Sequence of entity 1 (A, F), FASTA

>4MJI_1 HLA class I histocompatibility antigen, B-51 alpha chain (chains A, F)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRENLRIALRYYNQSEAGSHTWQTMYGCDVGPDGRLLRGHNQYAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAAREAEQLRAYLEGLCVEWLRRHLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G), FASTA

>4MJI_2 Beta-2-microglobulin (chains B, G)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>4MJI_3 HIV Reverse Transcriptase peptide Marker (chains C, H)
TAFTIPSI

Sequence of entity 4 (D, I), FASTA

>4MJI_4 T-Cell Receptor Chain alpha (chains D, I)
GEEDPQALSIQEGENATMNCSYKTSINNLQWYRQNSGRGLVHLILIRSNEREKHSGRLRV
TLDTSKKSSSLLITASRAADTASYFCATDDDSARQLTFGSGTQLTVLPDIQNPDPAVYQL
RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA
CANAFNNSIIPEDTF

Sequence of entity 5 (E, J), FASTA

>4MJI_5 T-cell Receptor Beta chain (chains E, J)
AGVSQTPSNKVTEKGKYVELRCDPISGHTALYWYRQSLGQGPEFLIYFQGTGAADDSGLP
NDRFFAVRPEGSVSTLKIQRTERGDSAVYLCASSLTGGGELFFGEGSRLTVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Primary citation

Molecular basis of a dominant T cell response to an HIV reverse transcriptase 8-mer epitope presented by the protective allele HLA-B*51:01. Motozono, C., Kuse, N., Sun, X. et al. J Immunol (2014) 192:3428-3434. DOI 10.4049/jimmunol.1302667 · PubMed

Other PDB entries of the same protein (UniProt P01889 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6MT3 1.21 Å, Crystal Structure of HLA-B*18:01 in complex with NP338 influenza peptide
3LN4 1.3 Å, Crystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from…
3BWA 1.3 Å, Crystal Structure of HLA B*3508 in complex with a HCMV 8-mer peptide from the pp65 protein
3SPV 1.3 Å, Crystal structure of a peptide-HLA complex
6MT6 1.31 Å, Crystal Structure of HLA-B*37:01 in complex with NP338 influenza peptide
2BVP 1.35 Å, Structures of Three HIV-1 HLA-B5703-Peptide Complexes and Identification of Related HLAs…
6MTL 1.35 Å, Crystal Structure of HLA-B*44:05 in complex with NP338 influenza peptide
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
6PYW 1.38 Å, Crystal Structure of HLA-B*2705-W60A in complex with LRN, a self-peptide

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