4N5E: 42F3 TCR pCPA12/H-2Ld complex

42F3 TCR pCPA12/H-2Ld complex. Determined by X-ray diffraction at 3.06 Å resolution. Released 19 Aug 2015.

Method: X-ray diffraction
Resolution: 3.06 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 4,947
Mol. weight: 72.79 kDa
Released: 19 Aug 2015

Explore 4N5E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4N5E contains 15 α-helices and 51 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	10
α-helix	13-14	2
β-strand	21-28	8	10
β-strand	31-37	7	10
β-strand	45-47	3	10
α-helix	51-54	4
α-helix	57-84	28
β-strand	94-103	10	10
β-strand	109-118	10	10
β-strand	121-126	6	10
β-strand	133-135	3	10
α-helix	139-150	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-173	10

Chain C: 3 helices, 19 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	44-49	6	2
β-strand	55-57	3	1
β-strand	62-67	6	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	87-93	7	2
β-strand	102-103	2	2
β-strand	107-112	6	2
β-strand	121-127	7	3
β-strand	134-139	6	3
β-strand	156-157	2	3
α-helix	158-160	3
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	170-172	3	4
β-strand	174-178	5	3
β-strand	199	1	3

Chain D: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	5
β-strand	10-14	5	6
β-strand	19-25	7	5
β-strand	31-38	8	6
β-strand	42-50	9	6
β-strand	56-57	2	6
β-strand	65-67	3	5
β-strand	73-78	6	5
α-helix	83-85	3
β-strand	87-96	10	6
β-strand	99-102	4	6
β-strand	106-111	6	6
β-strand	118	1	7
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	7
β-strand	152-158	7	8
β-strand	161-163	3	8
β-strand	167-169	3	3
β-strand	174-175	2	3
β-strand	185-194	10	3
α-helix	195-198	4
β-strand	204-211	8	8
β-strand	214	1	9
β-strand	228	1	9
β-strand	230-237	8	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
42F3 alpha VmCh	C	protein	212	Mus musculus, Homo sapiens	A0A0G2JFA3, P01738 (AlphaFold model), P01848 (AlphaFold model)
42F3 beta VmCh	D	protein	243	Mus musculus, Homo sapiens	A0A0A6YX08, A0A5B9
H-2 class I histocompatibility antigen, L-D alpha chain	A	protein	180	Mus musculus	P01897
pCPA12	B	protein	9

Sequence of entity 1 (C), FASTA

>4N5E_1 42F3 alpha VmCh (chains C)
GSHMAQSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQMLLKYYSGDPV
VQGVNGFEAEFSKSDSSFHLRKASVHWSDSAVYFCAVSAKGTGSKLSFGKGAKLTVSPNI
QNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSA
VAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (D), FASTA

>4N5E_2 42F3 beta VmCh (chains D)
MGEAAVTQSPRNKVTVTGGNVTLSCRQTNSHNYMYWYRQDTGHGLRLIHYSYGAGNLQIG
DVPDGYKATRTTQEDFFLLLELASPSQTSLYFCASSDAPGQLYFGEGSKLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Sequence of entity 3 (A), FASTA

>4N5E_3 H-2 class I histocompatibility antigen, L-D alpha chain (chains A)
MGPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEY
WERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYD
GCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATL

Sequence of entity 4 (B), FASTA

>4N5E_4 pCPA12 (chains B)
VPYMAEFGM

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 A0A0G2JFA3), best resolution first:

4MXQ 2.6 Å, 42F3 TCR pCPC5/H-2Ld Complex
4N0C 2.9 Å, 42F3 TCR pCPE3/H-2Ld complex
4MVB 3.09 Å, 42F3 pCPB7/H-2Ld Complex

Browse structure collections

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