6TDQ: Disulfide engineered HLA-A0201 molecule

Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GM dipeptide in the A pocket and one GM dipeptide in the F pocket. Determined by X-ray diffraction at 1.6 Å resolution. Released 25 Mar 2020.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,718
Mol. weight: 89.1 kDa
Ligands: GLY, MET
Released: 25 Mar 2020

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

Secondary structure: helices and β-sheets

6TDQ contains 27 α-helices and 60 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: 12 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	50-52	3
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	214-219	6	4
β-strand	222-223	2	4
α-helix	225-227	3
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	270-272	3	4

Chains B and D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	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	50-52	3
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
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
α-helix	225-227	3
β-strand	229-230	2	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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, C	protein	276	Homo sapiens	F6IQS1 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6TDQ_1 MHC class I antigen (chains A, C)
AGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGCYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMCAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWVAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B, D), FASTA

>6TDQ_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	4
MET	Methionine	C5 H11 N O2 S	4

Water and common crystallization additives (EDO, CL) are not listed.

Primary citation

Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection. Anjanappa, R., Garcia-Alai, M., Kopicki, J.D. et al. Nat Commun (2020) 11:1314-1314. DOI 10.1038/s41467-020-14862-4 · PubMed

Other PDB entries of the same protein (UniProt F6IQS1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TDP 1.4 Å, Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GL…
6TDO 1.65 Å, Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GM…
6TDS 1.7 Å, Crystal structure of the disulfide engineered HLA-A0201 molecule without peptide bound…
6TDR 1.75 Å, Crystal structure of the disulfide engineered HLA-A0201 molecule devoid of peptide…
33CG 2.2 Å, Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6
33CI 2.2 Å, Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-58
33CH 2.4 Å, Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-4

Browse structure collections

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