6EWA: HLA-A2

Crystal structure of HLA-A2 in complex with LILRB1. Determined by X-ray diffraction at 2.39 Å resolution. Released 7 Nov 2018.

Method: X-ray diffraction
Resolution: 2.39 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 8
Atoms: 9,148
Mol. weight: 132.88 kDa
Released: 7 Nov 2018

Explore 6EWA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EWA contains 35 α-helices and 107 β-strands across 6 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	50-53	4
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	133-134	2	1
α-helix	139-149	11
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
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	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	257-262	6	4
β-strand	270-273	4	4

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	7
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
β-strand	87	1	9
β-strand	91-94	4	8

Chain D: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	10
β-strand	15-17	3	11
β-strand	22-26	5	10
β-strand	38-39	2	12
α-helix	47-49	3
β-strand	61-62	2	10
α-helix	67-69	3
β-strand	71-74	4	12
α-helix	86-90	5
β-strand	91-93	3	12
β-strand	94-96	3	11
β-strand	99	1	9
β-strand	103-107	5	13
β-strand	111-113	3	14
β-strand	118-123	6	13
β-strand	126	1	5
β-strand	130-136	7	15
β-strand	143-147	5	15
β-strand	156-161	6	13
β-strand	171-177	7	15
β-strand	184	1	11
β-strand	185	1	15
α-helix	186-191	6
β-strand	192-193	2	15
β-strand	195-197	3	14

Chain E: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	16
α-helix	20	1
β-strand	21-28	8	16
β-strand	31-37	7	16
β-strand	46-47	2	16
α-helix	50-53	4
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	141-149	9
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	17
β-strand	186-195	10	18
β-strand	198-208	11	18
β-strand	209	1	17
β-strand	214-219	6	19
β-strand	222-223	2	19
α-helix	225-227	3
β-strand	228-230	3	18
α-helix	231-233	3
β-strand	234-235	2	18
β-strand	241-249	9	18
α-helix	254-256	3
β-strand	257-262	6	19
β-strand	270-272	3	19

Chain F: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	20
β-strand	3	1	21
α-helix	4-5	2
β-strand	6-11	6	22
β-strand	21-30	10	22
β-strand	31	1	21
β-strand	36-41	6	23
β-strand	44-45	2	23
α-helix	46	1
β-strand	50-51	2	22
α-helix	52-54	3
β-strand	55-56	2	22
β-strand	62-70	9	22
β-strand	78-83	6	23
β-strand	87	1	24
β-strand	91-94	4	23

Chain H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	25
β-strand	15-17	3	26
β-strand	22-27	6	25
β-strand	35-39	5	27
α-helix	45-47	3
α-helix	52-56	5
β-strand	59-62	4	25
α-helix	67-69	3
β-strand	71-77	7	27
β-strand	78-79	2	28
β-strand	83-84	2	28
α-helix	85-90	6
β-strand	91-93	3	27
β-strand	94-96	3	26
β-strand	99	1	24
β-strand	103-107	5	29
β-strand	111-113	3	30
β-strand	119-123	5	29
β-strand	126	1	20
β-strand	130-136	7	26
β-strand	144-147	4	26
β-strand	156-160	5	29
β-strand	171-177	7	26
β-strand	184-185	2	26
α-helix	187-191	5
β-strand	192-193	2	26
β-strand	195-197	3	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A, E	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, F	protein	99	Homo sapiens	P61769 (AlphaFold model)
Polyprotein	C, G	protein	9	Human immunodeficiency virus 1	P04585 (AlphaFold model)
LIR-1	D, H	protein	195	Homo sapiens	Q8NHL6 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>6EWA_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, E)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, F), FASTA

>6EWA_2 Beta-2-microglobulin (chains B, F)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, G), FASTA

>6EWA_3 Polyprotein (chains C, G)
ILKEPVHGV

Sequence of entity 4 (D, H), FASTA

>6EWA_4 LIR-1 (chains D, H)
PKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTAPWITRIPQELVKKGQFPIP
SITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVTLQCD
SQVAFDGFILCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSNSPY
EWSLPSDLLELLVLG

Primary citation

Application of the immunoregulatory receptor LILRB1 as a crystallisation chaperone for human class I MHC complexes. Mohammed, F., Stones, D.H., Willcox, B.E. J Immunol Methods (2019) 464:47-56. DOI 10.1016/j.jim.2018.10.011 · 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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