5C09: HLA class I histocompatibility antigen

HLA class I histocompatibility antigen. Determined by X-ray diffraction at 2.48 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 2.48 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,529
Mol. weight: 191.61 kDa
Released: 4 May 2016

Explore 5C09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C09 contains 51 α-helices and 143 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: 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	52-54	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	253-256	4
β-strand	257-262	6	4
β-strand	270-272	3	4

Chains B and G: 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	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
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: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	8
α-helix	10	1
β-strand	11-14	4	9
β-strand	19-25	7	8
β-strand	32-38	7	9
β-strand	45-51	7	9
β-strand	54-58	5	8
β-strand	61-66	6	8
β-strand	71-76	6	8
α-helix	81-83	3
β-strand	85-92	8	9
β-strand	100-101	2	9
β-strand	105-110	6	9
α-helix	111-112	2
β-strand	119-124	6	10
β-strand	125	1	11
β-strand	132-137	6	10
β-strand	154-162	9	10
β-strand	169-176	8	10
α-helix	186-188	3

Chain E: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	9
β-strand	19-24	6	12
α-helix	25-26	2
β-strand	31-37	7	9
β-strand	43-50	8	9
β-strand	53-56	4	9
β-strand	65-71	7	12
β-strand	74-79	6	12
α-helix	84-86	3
β-strand	88-95	8	9
α-helix	97-100	4
β-strand	106-107	2	9
β-strand	111-116	6	9
α-helix	119-121	3
β-strand	123	1	13
α-helix	124-125	2
β-strand	126-130	5	11
α-helix	131-133	3
α-helix	136-140	5
β-strand	142-152	11	11
β-strand	153	1	13
β-strand	157-163	7	14
β-strand	166-168	3	14
β-strand	172-174	3	11
β-strand	179-180	2	11
β-strand	190-199	10	11
α-helix	200-204	5
β-strand	210-216	7	14
β-strand	219	1	15
α-helix	230-231	2
β-strand	233	1	15
β-strand	235-241	7	14

Chain F: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	16
β-strand	15	1	17
β-strand	17	1	17
β-strand	21-28	8	16
β-strand	31-37	7	16
β-strand	46-47	2	16
α-helix	52-54	3
α-helix	57-84	28
β-strand	94-103	10	16
β-strand	109-118	10	16
β-strand	121-126	6	16
β-strand	133-135	3	16
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
α-helix	184-185	2
β-strand	186-195	10	18
β-strand	198-208	11	18
β-strand	214-219	6	19
β-strand	222-224	3	19
β-strand	229-230	2	18
α-helix	231-233	3
β-strand	234-235	2	18
β-strand	241-250	10	18
α-helix	253-256	4
β-strand	257-262	6	19
β-strand	270-272	3	19

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3

Chain I: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	23
β-strand	11-14	4	24
β-strand	19-25	7	23
β-strand	32-38	7	24
β-strand	45-51	7	24
β-strand	54-58	5	23
β-strand	61-66	6	23
β-strand	71-76	6	23
α-helix	81-83	3
β-strand	85-92	8	24
β-strand	100-101	2	24
β-strand	105-110	6	24
α-helix	111-112	2
β-strand	119-124	6	25
β-strand	125	1	26
β-strand	132-137	6	25
β-strand	144	1	27
β-strand	154-155	2	25
α-helix	156-158	3
β-strand	159-163	5	25
β-strand	168-176	9	25
β-strand	192	1	27

Chain J: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	28
β-strand	10-14	5	24
β-strand	19-24	6	28
α-helix	25-26	2
β-strand	31-37	7	24
β-strand	43-50	8	24
β-strand	53-56	4	24
β-strand	65-71	7	28
β-strand	74-79	6	28
α-helix	84-86	3
β-strand	88-95	8	24
α-helix	97-100	4
β-strand	106-107	2	24
β-strand	111-116	6	24
α-helix	119-121	3
β-strand	123	1	29
α-helix	124-125	2
β-strand	126-130	5	26
α-helix	131-133	3
α-helix	134-140	7
β-strand	142-152	11	26
β-strand	153	1	29
β-strand	157-163	7	30
β-strand	166-168	3	30
β-strand	172-174	3	26
α-helix	178	1
β-strand	179-180	2	26
β-strand	190-199	10	26
α-helix	200-204	5
β-strand	209-216	8	30
β-strand	219	1	31
α-helix	230-231	2
β-strand	233	1	31
β-strand	235-242	8	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A, F	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
Marker peptide	C, H	protein	10	Homo sapiens
1E6 TCR Alpha Chain	D, I	protein	200	Homo sapiens	A0A0B4J271 (AlphaFold model), P01848 (AlphaFold model)
1E6 TCR Beta Chain	E, J	protein	246	Homo sapiens	A0A0B4J2E0, A0A5B9

Sequence of entity 1 (A, F), FASTA

>5C09_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, F)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G), FASTA

>5C09_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>5C09_3 Marker peptide (chains C, H)
YLGGPDFPTI

Sequence of entity 4 (D, I), FASTA

>5C09_4 1E6 TCR Alpha Chain (chains D, I)
EVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQYSRKGPELLMYTYSSGNKEDGRFT
AQVDKSSKYISLFIRDSQPSDSATYLCAMRGDSSYKLIFGSGTRLLVRPDIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSP

Sequence of entity 5 (E, J), FASTA

>5C09_5 1E6 TCR Beta Chain (chains E, J)
DAGVIQSPRHEVTEMGQQVTLRCKPISGHDYLFWYRQTMMRGLELLIYFNNNVPIDDSGM
PEDRFSAKMPNASFSTLKIQPSEPRDSAVYFCASSLWEKLAKNIQYFGAGTRLSVLEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Primary citation

Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity. Cole, D.K., Bulek, A.M., Dolton, G. et al. J Clin Invest (2016) 126:2191-2204. DOI 10.1172/JCI85679 · 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

Browse structure collections

About this viewer

MolViewer shows 5C09 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.