4MS8: 42F3 TCR pCPB9/H-2Ld Complex

42F3 TCR pCPB9/H-2Ld Complex. Determined by X-ray diffraction at 1.92 Å resolution. Released 24 Sept 2014.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Mus musculus
Chains: 4
Atoms: 5,275
Mol. weight: 72.69 kDa
Released: 24 Sept 2014

Explore 4MS8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4MS8 contains 20 α-helices and 50 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	9
β-strand	21-28	8	9
β-strand	31-37	7	9
β-strand	46-47	2	9
α-helix	50-52	3
α-helix	57-83	27
β-strand	94-103	10	9
β-strand	109-118	10	9
β-strand	121-126	6	9
β-strand	133-135	3	9
α-helix	138-150	13
α-helix	152-161	10
α-helix	163-174	12

Chain C: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	9-13	5	2
β-strand	18-20	3	1
β-strand	23-24	2	1
β-strand	31-37	7	2
β-strand	43-49	7	2
β-strand	55-57	3	1
α-helix	59-61	3
β-strand	62-67	6	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	86-93	8	2
β-strand	102-103	2	2
β-strand	107-112	6	2
α-helix	113-114	2
β-strand	121-127	7	3
β-strand	134-139	6	3
α-helix	145-150	6
β-strand	156-157	2	3
α-helix	158-160	3
β-strand	161-165	5	3
α-helix	166-168	3
β-strand	170-178	9	3
α-helix	186-188	3
β-strand	199	1	3

Chain D: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-14	5	5
β-strand	19-25	7	4
β-strand	31-38	8	5
β-strand	42-49	8	5
β-strand	56-57	2	5
β-strand	65-68	4	4
β-strand	73-78	6	4
α-helix	83-85	3
β-strand	87-96	10	5
β-strand	99-102	4	5
β-strand	106-111	6	5
α-helix	114-116	3
β-strand	118	1	6
α-helix	119-120	2
β-strand	121-126	6	3
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	3
β-strand	148	1	6
β-strand	152-158	7	7
β-strand	161-163	3	7
β-strand	167-169	3	3
α-helix	173	1
β-strand	174-175	2	3
β-strand	185-194	10	3
α-helix	195-198	4
β-strand	204-211	8	7
β-strand	214	1	8
α-helix	225-226	2
β-strand	228	1	8
β-strand	230-237	8	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
42F3 alpha	C	protein	212	Mus musculus
42F3 beta	D	protein	243	Mus musculus
H-2 class I histocompatibility antigen, L-D alpha chain	A	protein	180	Mus musculus	P01897 (AlphaFold model)
pCPB9	B	protein	9

Sequence of entity 1 (C), FASTA

>4MS8_1 42F3 alpha (chains C)
GSHMAQSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQMLLKYYSGDPV
VQGVNGFEAEFSKSDSSFHLRKASVHWSDSAVYFCAVSAKGTGSKLSFGKGAKLTVSPNI
QNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSA
VAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (D), FASTA

>4MS8_2 42F3 beta (chains D)
MGEAAVTQSPRNKVTVTGGNVTLSCRQTNSHNYMYWYRQDTGHGLRLIHYSYGAGNLQIG
DVPDGYKATRTTQEDFFLLLELASPSQTSLYFCASSDAPGQLYFGEGSKLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Sequence of entity 3 (A), FASTA

>4MS8_3 H-2 class I histocompatibility antigen, L-D alpha chain (chains A)
MGPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEY
WERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYD
GCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATL

Sequence of entity 4 (B), FASTA

>4MS8_4 pCPB9 (chains B)
SPAEAGFFL

Primary citation

Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity. Adams, J.J., Narayanan, S., Birnbaum, M.E. et al. Nat Immunol (2016) 17:87-94. DOI 10.1038/ni.3310 · PubMed

Other PDB entries of the same protein (UniProt P01897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
6L9K 1.8 Å, H2-Ld a1a2 complexed with A5 peptide
8D5N 1.8 Å, Crystal structure of Ld-HF10
3VJ6 1.9 Å, Structure of the MHC class Ib molecule Qa-1b
3ERY 1.95 Å, Different thermodynamic binding mechanisms and peptide fine specificities associated…
5VCL 2.05 Å, Structure of the Qdm peptide bound to Qa-1a
3TJH 2.12 Å, 42F3-p3A1/H2-Ld complex
2OI9 2.35 Å, Structure of the 2C/Ld/QL9 allogeneic complex
6L9L 2.4 Å, 1D4 TCR recognition of H2-Ld a1a2 A5 Peptide Complexes

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