5MEN: Human Leukocyte Antigen A02 presenting ILAKFLHWL

Human Leukocyte Antigen A02 presenting ILAKFLHWL, in complex with cognate T-Cell Receptor. Determined by X-ray diffraction at 2.81 Å resolution. Released 7 Dec 2016.

Method: X-ray diffraction
Resolution: 2.81 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,739
Mol. weight: 94.97 kDa
Released: 7 Dec 2016

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

Secondary structure: helices and β-sheets

5MEN contains 22 α-helices and 76 β-strands across 4 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: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-12	11	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	50-53	4
α-helix	57-84	28
β-strand	94-104	11	1
β-strand	106-118	13	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	164-173	10
α-helix	176-179	4
β-strand	183	1	2
β-strand	187-193	7	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214	1	4
β-strand	217-219	3	5
β-strand	222-223	2	5
β-strand	230	1	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-261	5	5
β-strand	262	1	4
β-strand	270-273	4	5

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
β-strand	6-11	6	7
α-helix	14-15	2
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-45	2	8
β-strand	50-51	2	7
α-helix	52-54	3
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
β-strand	91-94	4	8
α-helix	95-96	2

Chain D: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-14	5	10
β-strand	19-25	7	9
β-strand	29-37	9	10
β-strand	43-48	6	10
β-strand	52-56	5	9
β-strand	59-64	6	9
β-strand	69-74	6	9
α-helix	79-81	3
β-strand	83-91	9	10
α-helix	99	1
β-strand	100-101	2	10
β-strand	105-110	6	10
α-helix	111-112	2
β-strand	119-125	7	11
β-strand	132-137	6	11
β-strand	153-155	3	11
α-helix	156-158	3
β-strand	161-163	3	12
β-strand	168-170	3	12
β-strand	172-177	6	11
β-strand	198	1	11

Chain E: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	10-14	5	14
β-strand	20-21	2	15
β-strand	22-24	3	13
β-strand	31-37	7	14
β-strand	43-51	9	14
β-strand	54-56	3	14
β-strand	64-66	3	15
β-strand	73	1	13
β-strand	76-78	3	15
α-helix	83-85	3
β-strand	87-94	8	14
β-strand	100-102	3	14
β-strand	106-111	6	14
β-strand	118	1	16
α-helix	119-120	2
β-strand	121-126	6	11
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	11
β-strand	148	1	16
β-strand	152-158	7	17
β-strand	161-163	3	17
β-strand	167-169	3	11
α-helix	173	1
β-strand	174-175	2	11
β-strand	185-194	10	11
α-helix	195-199	5
β-strand	204-211	8	17
β-strand	214	1	18
β-strand	228	1	18
β-strand	231-237	7	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Ile-leu-ala-lys-phe-leu-his-trp-leu	C	protein	9	Homo sapiens	O14746 (AlphaFold model)
Protein TRAV22,Human nkt tcr alpha chain	D	protein	200	Homo sapiens	A0A0B4J277 (AlphaFold model), K7N5M3
Protein TRBV6-5,Human nkt tcr beta chain	E	protein	240	Homo sapiens	A0A0K0K1A5, K7N5M4

Sequence of entity 1 (A), FASTA

>5MEN_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>5MEN_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>5MEN_3 ILE-LEU-ALA-LYS-PHE-LEU-HIS-TRP-LEU (chains C)
ILAKFLHWL

Sequence of entity 4 (D), FASTA

>5MEN_4 Protein TRAV22,Human nkt tcr alpha chain (chains D)
IQVEQSPPDLILQEGANSTLRCNFSDSVNNLQWFHQNPWGQLINLFYIPSGTKQNGRLSA
TTVATERYSLLYISSSQTTDSGVYFCAVDSATSGTYKYIFGTGTRLKVLANIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPS

Sequence of entity 5 (E), FASTA

>5MEN_5 Protein TRBV6-5,Human nkt tcr beta chain (chains E)
AGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVP
NGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYQGTEAFFGQGTRLTVVEDLNKVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Primary citation

Structural Mechanism Underpinning Cross-reactivity of a CD8+ T-cell Clone That Recognizes a Peptide Derived from Human Telomerase Reverse Transcriptase. Cole, D.K., van den Berg, H.A., Lloyd, A. et al. J Biol Chem (2017) 292:802-813. DOI 10.1074/jbc.M116.741603 · 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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