9C96: TAP binding protein related

Cryo-EM structure of TAP binding protein related (TAPBPR) in complex with HLA-A*02:01 bound to a suboptimal peptide. Determined by electron microscopy at 3.0 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,687
Mol. weight: 85.73 kDa
Released: 22 Jan 2025

Explore 9C96 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C96 contains 11 α-helices and 58 β-strands across 3 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: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	57-72	16
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	138-140	3
α-helix	141-150	10
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	183-185	3
β-strand	186-192	7	2
β-strand	199-208	10	2
β-strand	214-219	6	3
β-strand	222-223	2	3
α-helix	225-227	3
β-strand	228-230	3	2
β-strand	234-235	2	2
β-strand	241-249	9	2
β-strand	257-262	6	3
β-strand	270-272	3	3

Chain B: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	4
β-strand	6-11	6	5
β-strand	21-22	2	6
β-strand	23-30	8	5
β-strand	31	1	4
β-strand	37-41	5	2
β-strand	44-45	2	2
β-strand	50-51	2	5
α-helix	52-54	3
β-strand	55-56	2	5
β-strand	62-67	6	5
β-strand	69-70	2	6
β-strand	78-82	5	2
β-strand	91-94	4	2

Chain C: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	16-20	5	7
β-strand	37-41	5	7
β-strand	66	1	7
β-strand	99-104	6	7
β-strand	122-127	6	7
β-strand	133-135	3	7
β-strand	170-173	4	7
β-strand	178-182	5	8
α-helix	185-186	2
β-strand	187-188	2	9
β-strand	192-194	3	7
β-strand	203-210	8	8
β-strand	213-221	9	8
β-strand	233	1	9
β-strand	243-244	2	7
β-strand	248-249	2	9
α-helix	254-256	3
β-strand	258-265	8	8
β-strand	274-280	7	8
β-strand	281	1	10
β-strand	284-288	5	2
β-strand	297-305	9	2
β-strand	306	1	10
β-strand	311-316	6	11
β-strand	324-326	3	11
β-strand	330-331	2	2
β-strand	335-337	3	2
β-strand	342-349	8	2
β-strand	359-364	6	11
β-strand	372-375	4	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	277	Homo sapiens	Q8WLS4 (AlphaFold model)
Beta-2-microglobulin	B	protein	98	Homo sapiens	P61769 (AlphaFold model)
Tapasin-related protein	C	protein	384	Homo sapiens	Q9BX59 (AlphaFold model)
Lys-ile-leu-gly-phe-val	D	protein	7	Homo sapiens

Sequence of entity 1 (A), FASTA

>9C96_1 MHC class I antigen (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
CKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>9C96_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFCPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRD

Sequence of entity 3 (C), FASTA

>9C96_3 Tapasin-related protein (chains C)
KPHPAEGQWRAVDVVLDCFLVKDGAHRGALASSEDRARASLVLKQVPVLDDGSLEDFTDF
QGGTLAQDDPPIIFEASVDLVQIPQAEALLHADSSGKEVTCEIFRYFLQMTETTVKTAAW
FMANVQVSGGGPSISLVMKTPRVAKNEVLWHPTLNLPLSPQGTVRTAVEFQVMTQTQSLS
FLLGSSASLDCGFSMAPGLDLISVEWRLQHLGRGQLVYSWTAGQGQAVRKGATLEPAQLG
MARDASLTLPGLTIQDEGTYICQITTSLYQAQQIIQLNIQASPKVRLSLANEALLPTLIC
DIAGYYPLDVVVTWTREELGGSPAQVSGASFSSLRQSVAGTYSISSSLTAEPGSAGATYT
CQVTHISLEEPLGASTQVVPPERR

Sequence of entity 4 (D), FASTA

>9C96_4 LYS-ILE-LEU-GLY-PHE-VAL (chains D)
KILGFVF

Primary citation

CryoEM structure of an MHC-I/TAPBPR peptide-bound intermediate reveals the mechanism of antigen proofreading. Sun, Y., Pumroy, R.A., Mallik, L. et al. Proc Natl Acad Sci U S A (2025) 122:e2416992122-e2416992122. DOI 10.1073/pnas.2416992122 · PubMed

Other PDB entries of the same protein (UniProt Q8WLS4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9X7U 1.59 Å, Complex of HLA-A2, a class I MHC, with a UTP20 peptide
9WK0 1.8 Å, Neoantigen Rac1P29S-HLA-A2
21GJ 1.83 Å, Neoantigen p53Y220D-HLA-A2
21EX 2.02 Å, Wild tipe p53WT-HLA-A2
9XME 2.04 Å, Complex of HLA-A2, a class I MHC, with a wild type UTP20 peptide
9J4U 2.17 Å, Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by…
9PIX 2.35 Å, Mur14 Fab with HBV c18V pMHC
9PKC 2.5 Å, Mur35 Fab with HBV c18V pMHC
9PKF 2.6 Å, Mur35 Fab with HBV c18I pMHC
9PKV 2.72 Å, HU-38 Fab with PRAME pMHC
9LLU 2.87 Å, p53 epitope specific TCR 4414A binding to p53Y220D-HLA-A2
3HG1 3.0 Å, Germline-governed recognition of a cancer epitope by an immunodominant human T cell…

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