6Q3S: Engineered Human HLA_A2 MHC Class I molecule

Engineered Human HLA_A2 MHC Class I molecule in complex with TCR and SV9 peptide. Determined by X-ray diffraction at 2.5 Å resolution. Released 24 Jul 2019.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,626
Mol. weight: 94.62 kDa
Released: 24 Jul 2019

Explore 6Q3S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q3S contains 22 α-helices and 74 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
α-helix	19-20	2
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	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	133-135	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	186-195	10	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-218	5	4
β-strand	223	1	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-249	9	3
β-strand	258-262	5	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
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7
α-helix	95-96	2

Chain D: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	30-38	9	9
β-strand	44-51	8	9
β-strand	56-59	4	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-94	9	9
β-strand	103-104	2	9
β-strand	108-113	6	9
β-strand	122-127	6	10
β-strand	128	1	11
β-strand	135-140	6	10
α-helix	147-150	4
β-strand	156-158	3	10
β-strand	162-166	5	12
β-strand	171-175	5	12
β-strand	177-180	4	10

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
β-strand	9-13	5	14
β-strand	19-20	2	15
β-strand	21-24	4	13
β-strand	30-36	7	14
β-strand	42-48	7	14
β-strand	55-56	2	14
β-strand	63-65	3	15
β-strand	72	1	13
β-strand	75-77	3	15
α-helix	82-84	3
β-strand	86-93	8	14
β-strand	102-103	2	14
β-strand	107-112	6	14
α-helix	115-117	3
β-strand	119	1	16
β-strand	122-126	5	11
α-helix	127-129	3
α-helix	132-135	4
β-strand	139-148	10	11
β-strand	149	1	16
β-strand	153-159	7	17
β-strand	162-163	2	17
β-strand	168-170	3	11
α-helix	174	1
β-strand	175-176	2	11
α-helix	184-185	2
β-strand	186-194	9	11
α-helix	196-200	5
β-strand	205-212	8	17
β-strand	215	1	18
β-strand	229	1	18
β-strand	231-238	8	17

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)
Ser-leu-leu-met-trp-ile-thr-gln-val	C	protein	9	Homo sapiens
T cell receptor alpha variable 21,T-cell receptor, sp3.4 alpha chain	D	protein	207	Homo sapiens	A0A0B4J279 (AlphaFold model), K7N5N2 (AlphaFold model)
T cell receptor beta variable 6-5,Human nkt tcr beta chain	E	protein	241	Homo sapiens	A0A0K0K1A5, K7N5M4

Sequence of entity 1 (A), FASTA

>6Q3S_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGCYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMCAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>6Q3S_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6Q3S_3 SER-LEU-LEU-MET-TRP-ILE-THR-GLN-VAL (chains C)
SLLMWITQV

Sequence of entity 4 (D), FASTA

>6Q3S_4 T cell receptor alpha variable 21,T-cell receptor, sp3.4 alpha chain (chains D)
QEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGR
LNASLDKSSGRSTLYIAASQPGDSATYLCAVRPTSGGSYIPTFGRGTSLIVHPYIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>6Q3S_5 T cell receptor beta variable 6-5,Human nkt tcr beta chain (chains E)
GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPN
GYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYVGNTGELFFGEGSRLTVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Primary citation

High-throughput peptide-MHC complex generation and kinetic screenings of TCRs with peptide-receptive HLA-A*02:01 molecules. Moritz, A., Anjanappa, R., Wagner, C. et al. Sci Immunol (2019) 4. DOI 10.1126/sciimmunol.aav0860 · 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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