4N0C: 42F3 TCR pCPE3/H-2Ld complex

42F3 TCR pCPE3/H-2Ld complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 19 Aug 2015.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Mus musculus, Homo sapiens
Chains: 8
Atoms: 9,790
Mol. weight: 145.58 kDa
Released: 19 Aug 2015

Explore 4N0C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4N0C contains 25 α-helices and 103 β-strands across 6 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	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	45-47	3	1
α-helix	50-54	5
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	138-140	3
α-helix	141-149	9
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-172	9

Chain C: 1 helix, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	2
β-strand	9-13	5	3
β-strand	18-20	3	2
β-strand	23-24	2	2
β-strand	31-37	7	3
β-strand	43-49	7	3
β-strand	55-57	3	2
β-strand	62-67	6	2
β-strand	72-77	6	2
α-helix	82-84	3
β-strand	87-93	7	3
β-strand	102-103	2	3
β-strand	107-112	6	3
β-strand	121-125	5	4
β-strand	126-127	2	5
β-strand	135-139	5	4
β-strand	156-158	3	4
β-strand	163-165	3	6
β-strand	170-172	3	6
β-strand	174-178	5	4

Chain D: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-14	5	3
β-strand	19-25	7	7
β-strand	31-38	8	3
β-strand	42-50	9	3
β-strand	56-57	2	3
β-strand	65-67	3	7
β-strand	73-78	6	7
α-helix	83-85	3
β-strand	88-96	9	3
β-strand	99-102	4	3
β-strand	106-111	6	3
α-helix	114-116	3
β-strand	118	1	8
β-strand	121-126	6	5
α-helix	129-135	7
β-strand	137-147	11	5
β-strand	148	1	8
β-strand	152-158	7	9
β-strand	161-163	3	9
β-strand	167-169	3	5
β-strand	174-175	2	5
β-strand	185-194	10	5
α-helix	195-199	5
β-strand	204-211	8	9
β-strand	214	1	10
β-strand	228	1	10
β-strand	230-237	8	9

Chain E: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	11
α-helix	13-14	2
β-strand	21-28	8	11
β-strand	31-37	7	11
β-strand	46	1	11
α-helix	51-54	4
α-helix	57-84	28
β-strand	94-103	10	11
β-strand	109-118	10	11
β-strand	121-126	6	11
β-strand	133-135	3	11
α-helix	138-140	3
α-helix	141-149	9
α-helix	152-157	6
α-helix	158-164	7
α-helix	165-172	8

Chain G: 1 helix, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	12
β-strand	9-13	5	13
β-strand	18-20	3	12
β-strand	23-24	2	12
β-strand	31-37	7	13
β-strand	44-49	6	13
β-strand	55-57	3	12
β-strand	62-67	6	12
β-strand	72-77	6	12
α-helix	82-84	3
β-strand	87-93	7	13
β-strand	102-103	2	13
β-strand	107-112	6	13
β-strand	121-126	6	14
β-strand	127	1	15
β-strand	134-139	6	14
β-strand	156-157	2	14
β-strand	163-165	3	16
β-strand	170-172	3	16
β-strand	174-178	5	14
β-strand	199	1	14

Chain H: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-14	5	18
β-strand	19-25	7	17
β-strand	31-38	8	18
β-strand	42-50	9	18
β-strand	56-57	2	18
β-strand	65-67	3	17
β-strand	73-78	6	17
α-helix	83-85	3
β-strand	88-96	9	18
β-strand	99-102	4	18
β-strand	106-111	6	18
β-strand	118	1	19
β-strand	121-125	5	15
α-helix	129-135	7
β-strand	137-147	11	15
β-strand	148	1	19
β-strand	152-158	7	20
β-strand	161-163	3	20
β-strand	167-169	3	15
β-strand	174-175	2	15
β-strand	185-194	10	15
α-helix	195-199	5
β-strand	204-211	8	20
β-strand	214	1	21
α-helix	225-226	2
β-strand	228	1	21
β-strand	230-237	8	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, L-D alpha chain	A, E	protein	180	Mus musculus	P01897 (AlphaFold model)
pCPE3	B, F	protein	9
42F3 VmCh alpha	C, G	protein	212	Mus musculus, Homo sapiens	A0A0G2JFA3, P01738 (AlphaFold model), P01848 (AlphaFold model)
42F3 VmCh beta	D, H	protein	243	Mus musculus, Homo sapiens	A0A0A6YX08, A0A5B9

Sequence of entity 1 (A, E), FASTA

>4N0C_1 H-2 class I histocompatibility antigen, L-D alpha chain (chains A, E)
MGPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEY
WERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYD
GCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATL

Sequence of entity 2 (B, F), FASTA

>4N0C_2 pCPE3 (chains B, F)
MPAGRPWDL

Sequence of entity 3 (C, G), FASTA

>4N0C_3 42F3 VmCh alpha (chains C, G)
GSHMAQSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQMLLKYYSGDPV
VQGVNGFEAEFSKSDSSFHLRKASVHWSDSAVYFCAVSAKGTGSKLSFGKGAKLTVSPNI
QNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSA
VAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D, H), FASTA

>4N0C_4 42F3 VmCh beta (chains D, H)
MGEAAVTQSPRNKVTVTGGNVTLSCRQTNSHNYMYWYRQDTGHGLRLIHYSYGAGNLQIG
DVPDGYKATRTTQEDFFLLLELASPSQTSLYFCASSDAPGQLYFGEGSKLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

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
4MS8 1.92 Å, 42F3 TCR pCPB9/H-2Ld Complex
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

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