5EUO: PF6-M1-HLA-A2

PF6-M1-HLA-A2. Determined by X-ray diffraction at 2.1 Å resolution. Released 23 Nov 2016.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 10
Atoms: 13,444
Mol. weight: 189.96 kDa
Released: 23 Nov 2016

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

Secondary structure: helices and β-sheets

5EUO contains 42 α-helices and 144 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: 9 helices, 18 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	50-54	5
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
β-strand	188-193	6	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-216	3	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	259-262	4	4
β-strand	270-272	3	4

Chain B: 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 C: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
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	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
β-strand	228-230	3	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
β-strand	50-51	2	13
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
α-helix	90	1
β-strand	91-94	4	14

Chain E: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	15
β-strand	11-15	5	16
β-strand	20-25	6	15
β-strand	30-38	9	16
β-strand	45-50	6	16
β-strand	56-59	4	15
β-strand	62-66	5	15
β-strand	72-77	6	15
β-strand	86-94	9	16
α-helix	95-97	3
β-strand	103-104	2	16
β-strand	108-113	6	16
β-strand	122-127	6	17
β-strand	128	1	18
β-strand	135-140	6	17
α-helix	148-151	4
β-strand	156-158	3	17
β-strand	162-166	5	17
β-strand	171-180	10	17

Chain F: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	19
β-strand	8-12	5	20
β-strand	17-19	3	21
β-strand	22-23	2	19
β-strand	29-35	7	20
β-strand	42-49	8	20
β-strand	52-55	4	20
β-strand	62-64	3	21
β-strand	71	1	19
β-strand	74-76	3	21
β-strand	85-92	8	20
β-strand	100-101	2	20
β-strand	105-110	6	20
α-helix	113-115	3
β-strand	117	1	22
α-helix	118-119	2
β-strand	120-124	5	18
α-helix	125-127	3
α-helix	128-134	7
β-strand	136-146	11	18
β-strand	147	1	22
β-strand	151-157	7	23
β-strand	160-162	3	23
β-strand	166-168	3	18
β-strand	173-174	2	18
β-strand	184-193	10	18
α-helix	194-197	4
β-strand	203-210	8	23
β-strand	213	1	24
α-helix	224-225	2
β-strand	227	1	24
β-strand	229-236	8	23

Chain G: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	25
β-strand	11-15	5	26
β-strand	20-25	6	25
β-strand	30-38	9	26
β-strand	45-50	6	26
β-strand	56-59	4	25
β-strand	62-66	5	25
β-strand	72-77	6	25
α-helix	82-84	3
β-strand	86-94	9	26
β-strand	103-104	2	26
β-strand	108-113	6	26
β-strand	122-128	7	27
β-strand	135-140	6	27
α-helix	149-151	3
β-strand	157-158	2	27
α-helix	159-161	3
β-strand	162-166	5	27
β-strand	171-179	9	27
α-helix	187-189	3

Chain H: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	28
β-strand	8-12	5	29
β-strand	17-19	3	30
β-strand	20-23	4	28
β-strand	29-35	7	29
β-strand	41-47	7	29
β-strand	54-55	2	29
β-strand	62-64	3	30
β-strand	71	1	28
β-strand	74-76	3	30
β-strand	85-92	8	29
α-helix	98-99	2
β-strand	100-101	2	29
β-strand	105-110	6	29
α-helix	113-115	3
β-strand	117	1	31
β-strand	120-125	6	27
α-helix	126-127	2
α-helix	128-133	6
β-strand	136-146	11	27
β-strand	147	1	31
β-strand	151-157	7	32
β-strand	160-162	3	32
β-strand	166-168	3	27
α-helix	172	1
β-strand	173-174	2	27
β-strand	184-193	10	27
α-helix	194-197	4
β-strand	203-210	8	32
β-strand	213	1	33
β-strand	227	1	33
β-strand	229-236	8	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A, C	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)
PF6 TCR alpha chain	E, G	protein	208	Homo sapiens
PF6 TCR beta chain	F, H	protein	240	Homo sapiens
Matrix protein 1	I, J	protein	9	Influenza A virus	P03485 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5EUO_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, C)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B, D), FASTA

>5EUO_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, G), FASTA

>5EUO_3 PF6 TCR alpha chain (chains E, G)
MTQLLEQSPQFLSIQEGENLTVYCNSSSVFSSLQWYRQEPGEGPVLLVTVVTGGEVKKLK
RLTFQFGDARKDSSLHITAAQPGDTGLYLCAGAIGPSNTGKLIFGKGTKLSVKPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>5EUO_4 PF6 TCR beta chain (chains F, H)
GITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDIAE
GYSVSREKKESFPLTVTSAQANPTAFYLCASSIRSSYEQYFGPGTRLTVTEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Sequence of entity 5 (I, J), FASTA

>5EUO_5 Matrix protein 1 (chains I, J)
GILGFVFTL

Primary citation

Crystal structure of PF6-M1-HLA-A2 complex. Yang, X., Mariuzza, R.A. To be published.

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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