5EU6: HLA Class I antigen

HLA Class I antigen. Determined by X-ray diffraction at 2.02 Å resolution. Released 2 Mar 2016.

Method: X-ray diffraction
Resolution: 2.02 Å
Organisms: Homo sapiens, synthetic construct
Chains: 5
Atoms: 6,980
Mol. weight: 95.85 kDa
Released: 2 Mar 2016

Explore 5EU6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EU6 contains 25 α-helices and 71 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	138-149	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	222-223	2	4
β-strand	228-230	3	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

Chain B: 3 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	44-45	2	7
α-helix	46	1
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

Chain D: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	8
β-strand	11-15	5	9
β-strand	20-26	7	8
β-strand	33-39	7	9
β-strand	46-52	7	9
β-strand	57-60	4	8
β-strand	63-68	6	8
β-strand	73-78	6	8
α-helix	83-85	3
β-strand	87-95	9	9
β-strand	102-105	4	9
β-strand	109-114	6	9
α-helix	115-116	2
β-strand	123	1	10
β-strand	127-128	2	10
β-strand	134-139	6	10
β-strand	157-159	3	10
α-helix	160-162	3
β-strand	163-166	4	10
β-strand	171-179	9	10

Chain E: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	11
β-strand	11-15	5	12
β-strand	20-25	6	11
β-strand	32-38	7	12
β-strand	45-51	7	12
β-strand	54-57	4	12
β-strand	66-69	4	11
β-strand	76-80	5	11
α-helix	85-87	3
β-strand	89-96	8	12
α-helix	103-104	2
β-strand	105-106	2	12
β-strand	110-115	6	12
α-helix	118-120	3
β-strand	122	1	13
α-helix	123-124	2
β-strand	125-129	5	14
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	14
β-strand	152	1	13
β-strand	156-162	7	15
β-strand	165-167	3	15
β-strand	171-173	3	14
α-helix	177	1
β-strand	178-179	2	14
β-strand	189-198	10	14
α-helix	199-202	4
β-strand	208-215	8	15
β-strand	218	1	16
α-helix	229-230	2
β-strand	232	1	16
β-strand	234-241	8	15

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)
Tyr-leu-glu-pro-gly-pro-val-thr-val	C	protein	9	synthetic construct	P40967 (AlphaFold model)
Human TCR Light Chain	D	protein	204	Homo sapiens	A0A0B4J279 (AlphaFold model), P01848
Human TCR Heavy Chain	E	protein	244	Homo sapiens	A0A592, A0A5B9

Sequence of entity 1 (A), FASTA

>5EU6_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>5EU6_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>5EU6_3 TYR-LEU-GLU-PRO-GLY-PRO-VAL-THR-VAL (chains C)
YLEPGPVTV

Sequence of entity 4 (D), FASTA

>5EU6_4 Human TCR Light Chain (chains D)
MKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTS
GRLNASLDKSSGRSTLYIAASQPGDSATYLCAVLSSGGSNYKLTFGKGTLLTVNPNIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFS

Sequence of entity 5 (E), FASTA

>5EU6_5 Human TCR Heavy Chain (chains E)
GAGVSQTPSNKVTEKGKYVELRCDPISGHTALYWYRQSLGQGPEFLIYFQGTGAADDSGL
PNDRFFAVRPEGSVSTLKIQRTERGDSAVYLCASSFIGGTDTQYFGPGTRLTVLEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Primary citation

A Molecular Switch Abrogates Glycoprotein 100 (gp100) T-cell Receptor (TCR) Targeting of a Human Melanoma Antigen. Bianchi, V., Bulek, A., Fuller, A. et al. J Biol Chem (2016) 291:8951-8959. DOI 10.1074/jbc.M115.707414 · 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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