5WER: TAPBPR and H2-Dd complex

Crystal Structure of TAPBPR and H2-Dd complex. Determined by X-ray diffraction at 3.41 Å resolution. Released 18 Oct 2017.

Method: X-ray diffraction
Resolution: 3.41 Å
Organisms: Mus musculus, Homo sapiens
Chains: 12
Atoms: 20,155
Mol. weight: 346.59 kDa
Ligands: CIT
Released: 18 Oct 2017

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

Secondary structure: helices and β-sheets

5WER contains 42 α-helices and 235 β-strands across 12 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, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-36	6	1
α-helix	52-54	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	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
β-strand	188-191	4	2
α-helix	195-197	3
β-strand	201-208	8	2
β-strand	214-215	2	3
β-strand	218	1	4
β-strand	230	1	2
β-strand	234-235	2	2
β-strand	241-247	7	2
β-strand	258	1	4
β-strand	261-262	2	3

Chain B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-11	6	6
β-strand	17	1	7
β-strand	19	1	7
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	37-41	5	8
β-strand	44-45	2	8
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-82	5	8
β-strand	91-94	4	8

Chain C: 3 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	9
β-strand	19-20	2	9
β-strand	41-47	7	9
β-strand	66-69	4	9
β-strand	99-105	7	9
β-strand	120-127	8	9
β-strand	133-139	7	9
α-helix	140-143	4
β-strand	159	1	10
β-strand	163	1	10
β-strand	166-174	9	9
β-strand	178-181	4	11
β-strand	186-189	4	12
β-strand	192-195	4	9
β-strand	201-210	10	11
β-strand	213-220	8	11
β-strand	225-227	3	11
β-strand	242-244	3	9
β-strand	247-251	5	12
α-helix	254-256	3
β-strand	258-266	9	11
β-strand	270-279	10	11
β-strand	281	1	13
α-helix	282-283	2
β-strand	284-285	2	2
β-strand	288-290	3	2
β-strand	297-305	9	2
β-strand	306	1	13
β-strand	311-312	2	14
β-strand	315-316	2	15
β-strand	331	1	8
β-strand	335-336	2	2
β-strand	342-349	8	2
β-strand	359-360	2	15
β-strand	363-364	2	14

Chain D: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	16
β-strand	18-28	11	16
β-strand	31-33	3	16
β-strand	35	1	17
β-strand	46	1	17
α-helix	52-54	3
α-helix	57-84	28
β-strand	94-104	11	16
β-strand	108-118	11	16
β-strand	121-126	6	16
β-strand	133-135	3	16
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	186-189	4	18
β-strand	198-208	11	18
α-helix	225-227	3
β-strand	229-230	2	18
β-strand	234-235	2	18
β-strand	241-250	10	18
β-strand	259-260	2	19
β-strand	271-272	2	19

Chain E: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	20
α-helix	4-5	2
β-strand	6-11	6	21
α-helix	14-15	2
β-strand	21-30	10	21
β-strand	31	1	20
β-strand	36-41	6	22
β-strand	44-45	2	22
α-helix	46	1
β-strand	50-51	2	23
α-helix	52-54	3
β-strand	55-56	2	21
β-strand	62-65	4	21
β-strand	66-67	2	23
β-strand	68-70	3	21
β-strand	79-83	5	22
β-strand	92-94	3	22

Chain F: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	24
β-strand	20	1	25
β-strand	41-43	3	24
β-strand	67-68	2	24
β-strand	100-103	4	25
β-strand	120-126	7	25
β-strand	133-139	7	25
β-strand	167-174	8	25
β-strand	178-182	5	26
β-strand	188-189	2	27
β-strand	192-195	4	25
β-strand	204-210	7	26
β-strand	213-220	8	26
β-strand	233	1	27
β-strand	242-244	3	25
β-strand	247-248	2	27
α-helix	254-256	3
β-strand	258-265	8	26
β-strand	270-280	11	26
β-strand	284-289	6	18
β-strand	298-303	6	18
β-strand	312-315	4	28
β-strand	325	1	28
β-strand	330	1	18
β-strand	331-332	2	22
β-strand	335-336	2	18
β-strand	342-348	7	18
β-strand	360-363	4	28
β-strand	372-373	2	28

Chain G: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	29
α-helix	20	1
β-strand	21-28	8	29
β-strand	31-35	5	29
β-strand	37	1	29
β-strand	46-47	2	29
α-helix	52-54	3
α-helix	57-84	28
β-strand	94-102	9	29
β-strand	111-118	8	29
β-strand	121-126	6	29
β-strand	133-135	3	29
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-173	9
β-strand	185-190	6	30
β-strand	199-207	9	30
β-strand	214-216	3	31
β-strand	228	1	30
β-strand	229-230	2	32
β-strand	234-236	3	30
β-strand	240-249	10	30
β-strand	259	1	33
β-strand	260-262	3	31
β-strand	272	1	33

Chain H: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	34
α-helix	4-5	2
β-strand	6-11	6	35
β-strand	21-30	10	35
β-strand	31	1	34
β-strand	36-41	6	36
β-strand	44-45	2	36
β-strand	50	1	35
β-strand	55-56	2	35
β-strand	62-70	9	35
β-strand	78-83	6	36
β-strand	91-94	4	36

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-D alpha chain	A, D, G, J	protein	277	Mus musculus	P01900 (AlphaFold model)
Beta-2-microglobulin	B, E, H, K	protein	100	Homo sapiens	P61769 (AlphaFold model)
TAP binding protein related	C, F, I, L	protein	394	Homo sapiens	Q9BX59 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>5WER_1 H-2 class I histocompatibility antigen, D-D alpha chain (chains A, D, G, J)
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYW
ERETRRAKGNEQCFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDG
CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLL
RTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGT
FQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGKE

Sequence of entity 2 (B, E, H, K), FASTA

>5WER_2 Beta-2-microglobulin (chains B, E, H, K)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F, I, L), FASTA

>5WER_3 TAP binding protein related (chains C, F, I, L)
KPHPAEGQWRAVDVVLDCFLVKDGAHRGALASSEDRARASLVLKQVPVLDDGSLEDFTDF
QGGTLAQDDPPIIFEASVDLVQIPQAEALLHADCSGKEVTCEISRYFLQMTETTVKTAAW
FMANVQVSGGGPSISLVMKTPRVAKNEVLWHPTLNLPLSPQGTVRTAVEFQVMTQTQSLS
FLLGSSASLDCGFSMAPGLDLISVEWRLQHKGRGQLVYSWTAGQGQAVRKGATLEPAQLG
MARDASLTLPGLTIQDEGTYICQITTSLYRAQQIIQLNIQASPKVRLSLANEALLPTLIC
DIAGYYPLDVVVTWTREELGGSPAQVSGASFSSLRQSVAGTYSISSSLTAEPGSAGATYT
CQVTHISLEEPLGASTQVVPPERRLEGGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1

Water and common crystallization additives (1PE, GOL, EDO) are not listed.

Primary citation

Crystal structure of a TAPBPR-MHC I complex reveals the mechanism of peptide editing in antigen presentation. Jiang, J., Natarajan, K., Boyd, L.F. et al. Science (2017) 358:1064-1068. DOI 10.1126/science.aao5154 · PubMed

Other PDB entries of the same protein (UniProt P01900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WEU 1.58 Å, Crystal Structure of H2-Dd with disulfide-linked 10mer peptide
3ECB 1.7 Å, Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human…
8FHU 1.8 Å, Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by…
5T7G 1.96 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
3E6H 2.1 Å, MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide,…
5IVX 2.1 Å, Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex
8FHL 2.19 Å, Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented…
1QO3 2.3 Å, Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd
8D5F 2.31 Å, The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd
5KD7 2.35 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
6NPR 2.37 Å, Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide…
1BII 2.4 Å, The crystal structure of H-2DD MHC class I in complex with the HIV-1 derived peptide…

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