5E9D: RD-1 Mart-1 High

RD-1 Mart-1 High bound to Mart-1 decameric peptide (ELA) in complex with HLA-A2. Determined by X-ray diffraction at 2.51 Å resolution. Released 8 Jun 2016.

Method: X-ray diffraction
Resolution: 2.51 Å
Organism: Homo sapiens
Chains: 10
Atoms: 9,683
Mol. weight: 151.79 kDa
Released: 8 Jun 2016

Explore 5E9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E9D contains 31 α-helices and 107 β-strands across 8 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, 18 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	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	214-217	4	4
β-strand	229-230	2	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	258-262	5	4
β-strand	270-273	4	4

Chains B and G: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
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
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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	8
β-strand	10-13	4	9
α-helix	17	1
β-strand	18-24	7	8
β-strand	31-37	7	9
β-strand	44-49	6	9
β-strand	53-57	5	8
β-strand	60-65	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-91	8	9
α-helix	97-98	2
β-strand	99-100	2	9
β-strand	104-109	6	9

Chain E: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-14	5	11
β-strand	19-21	3	12
β-strand	22-25	4	10
β-strand	31-38	8	11
β-strand	42-51	10	11
β-strand	54-57	4	11
β-strand	64-66	3	12
β-strand	73	1	10
β-strand	76-78	3	12
α-helix	83-85	3
β-strand	87-94	8	11
α-helix	97-99	3
β-strand	105-106	2	11
β-strand	110-115	6	11

Chain F: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	13
α-helix	20	1
β-strand	21-28	8	13
β-strand	31-37	7	13
β-strand	46-47	2	13
α-helix	57-84	28
β-strand	94-103	10	13
β-strand	109-118	10	13
β-strand	121-126	6	13
β-strand	133-135	3	13
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	14
α-helix	184-185	2
β-strand	186-193	8	15
β-strand	199-208	10	15
β-strand	209	1	14
β-strand	214-219	6	16
β-strand	222-223	2	16
β-strand	229-230	2	15
α-helix	231-233	3
β-strand	234-235	2	15
β-strand	241-249	9	15
α-helix	254-256	3
β-strand	257-262	6	16
β-strand	270-272	3	16

Chain I: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	20
β-strand	10-12	3	21
β-strand	18-24	7	20
β-strand	31-37	7	21
β-strand	44-49	6	21
β-strand	53-57	5	20
β-strand	60-65	6	20
β-strand	70-75	6	20
α-helix	80-82	3
β-strand	84-91	8	21
α-helix	97-98	2
β-strand	99-100	2	21
β-strand	104-108	5	21

Chain J: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	22
β-strand	10-13	4	23
β-strand	19-21	3	24
β-strand	22-25	4	22
β-strand	31-38	8	23
β-strand	42-51	10	23
β-strand	54-57	4	23
β-strand	64-66	3	24
β-strand	73	1	22
β-strand	76-78	3	24
α-helix	83-85	3
β-strand	87-94	8	23
α-helix	97-99	3
β-strand	105-106	2	23
β-strand	110-114	5	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A, F	protein	275	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
Melanoma derived Mart-1 peptide	C, H	protein	10	Homo sapiens	Q16655 (AlphaFold model)
A6-TCR Valpha	D, I	protein	129	Homo sapiens	A0A075B6T6 (AlphaFold model)
A6-TCR Vbeta	E, J	protein	156	Homo sapiens	A0A0K0K1A5

Sequence of entity 1 (A, F), FASTA

>5E9D_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, F)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B, G), FASTA

>5E9D_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>5E9D_3 Melanoma derived Mart-1 peptide (chains C, H)
ELAGIGILTV

Sequence of entity 4 (D, I), FASTA

>5E9D_4 A6-TCR Valpha (chains D, I)
QKEVEQNSGPLSVPEGAIASLNCTYSDRGSTSFFWYRQYSGKSPELIMSIYSNGDKEDGR
FTAQLNKASQYVSLLIRDSQPSDSATYLCAVTKYSWGKLQFGAGTQVVVTPDGGGLNDIF
EAQKIEWHE

Sequence of entity 5 (E, J), FASTA

>5E9D_5 A6-TCR Vbeta (chains E, J)
MGSSHHHHHHSSGLVPRGSNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMAWYRQDPGM
GLRLIHYSVGVGITDQGDVPDGYKVSRSTTEDFPLRLLSAAPSQTSVYFCASRPGWMAGG
VELYFGPGTRLTVTEDLINGSADDAKKDAAKKDGKS

Primary citation

An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry. Harris, D.T., Singh, N.K., Cai, Q. et al. Structure (2016) 24:1142-1154. DOI 10.1016/j.str.2016.04.011 · 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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