6R2L: NYBR1-A2-slskildtv

NYBR1-A2-slskildtv. Determined by X-ray diffraction at 2.3 Å resolution. Released 26 Feb 2020.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,152
Mol. weight: 95.89 kDa
Released: 26 Feb 2020

Explore 6R2L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6R2L contains 24 α-helices and 73 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	20	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	140-149	10
α-helix	152-161	10
α-helix	163-174	12
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	214-219	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

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
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, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	8
β-strand	11-15	5	9
β-strand	20-26	7	8
β-strand	32-38	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
β-strand	101-102	2	9
β-strand	106-111	6	9
β-strand	121-126	6	10
β-strand	133-137	5	10
α-helix	148-149	2
β-strand	155-156	2	10
α-helix	157-159	3
β-strand	160-164	5	11
β-strand	169-173	5	11
β-strand	174-177	4	10

Chain E: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	12
β-strand	11-15	5	13
β-strand	20-25	6	12
α-helix	26-27	2
β-strand	32-38	7	13
β-strand	45-51	7	13
β-strand	55-57	3	13
β-strand	66-70	5	12
β-strand	76-80	5	12
α-helix	85-87	3
β-strand	89-96	8	13
β-strand	99	1	14
β-strand	103	1	14
β-strand	109-110	2	13
β-strand	114-119	6	13
α-helix	122-124	3
β-strand	126	1	15
α-helix	127-128	2
β-strand	129-134	6	10
α-helix	135-136	2
α-helix	137-143	7
β-strand	145-155	11	10
β-strand	156	1	15
β-strand	160-166	7	16
β-strand	169-171	3	16
β-strand	175-177	3	10
β-strand	182-183	2	10
β-strand	193-202	10	10
α-helix	203-206	4
β-strand	213-219	7	16
β-strand	222	1	17
α-helix	233-234	2
β-strand	236	1	17
β-strand	238-244	7	16

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-ser-lys-ile-leu-asp-thr-val	C	protein	9	Homo sapiens	Q9BXX3 (AlphaFold model)
T cell receptor alpha variable 22,Human nkt tcr alpha chain	D	protein	194	Homo sapiens	A0A0B4J277 (AlphaFold model), K7N5M3
T cell receptor beta variable 11-2,Human nkt tcr beta chain	E	protein	247	Homo sapiens	A0A584, K7N5M4

Sequence of entity 1 (A), FASTA

>6R2L_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>6R2L_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6R2L_3 SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL (chains C)
SLSKILDTV

Sequence of entity 4 (D), FASTA

>6R2L_4 T cell receptor alpha variable 22,Human nkt tcr alpha chain (chains D)
MGIQVEQSPPDLILQEGANSTLRCNFSDSVNNLQWFHQNPWGQLINLFYIPSGWKQEGRL
SATTVATERYSLLYISSSQTTDSGVYFCAVGGNDWNTDKLIFGTGTRLQVFPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSII

Sequence of entity 5 (E), FASTA

>6R2L_5 T cell receptor beta variable 11-2,Human nkt tcr beta chain (chains E)
AGVAQSPRYKIIEKRQSVAFWCNPIFSHPTLYWYQQILGQGPKLLIQFGGWPGVDDSQLP
KDRFSAERLKGVDSTLKIQPAKLEDSALYLCASSPLDVSISSYNEQFFGPGTRLTVLEDL
KNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPL
KEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSA
EAWGRAD

Primary citation

Specificity of bispecific T cell receptors and antibodies targeting peptide-HLA. Holland, C.J., Crean, R.M., Pentier, J.M. et al. J Clin Invest (2020) 130:2673-2688. DOI 10.1172/JCI130562 · 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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