3TF7: 42F3 QL9/H2-Ld complex

42F3 QL9/H2-Ld complex. Determined by X-ray diffraction at 2.75 Å resolution. Released 7 Dec 2011.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Mus musculus
Chains: 8
Atoms: 10,138
Mol. weight: 154.43 kDa
Released: 7 Dec 2011

Explore 3TF7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3TF7 contains 26 α-helices and 121 β-strands across 8 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	7
α-helix	20	1
β-strand	21-28	8	7
β-strand	31-37	7	7
β-strand	46-47	2	7
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	7
β-strand	111-118	8	7
β-strand	121-126	6	7
β-strand	133-135	3	7
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-172	9

Chains B and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7

Chain C: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	2
β-strand	9-13	5	3
β-strand	18-20	3	2
β-strand	23-25	3	2
β-strand	31-37	7	3
β-strand	44-49	6	3
β-strand	55-57	3	2
β-strand	63-67	5	2
β-strand	72-77	6	2
α-helix	82-84	3
β-strand	87-93	7	3
β-strand	101-103	3	3
β-strand	107-112	6	3
β-strand	137-139	3	4
β-strand	143-147	5	5
β-strand	152-154	3	6
β-strand	156-158	3	4
β-strand	164-170	7	5
β-strand	176-183	8	5
β-strand	189-190	2	5
β-strand	198-200	3	6
β-strand	206	1	4
β-strand	208-211	4	6
α-helix	216-218	3
β-strand	220-229	10	5
β-strand	232-235	4	5
β-strand	239-244	6	5
α-helix	246-249	4

Chain E: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
β-strand	18-28	11	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	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	164-173	10

Chain G: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	8
β-strand	9-12	4	9
β-strand	18-20	3	8
β-strand	23-25	3	8
β-strand	31-37	7	9
β-strand	44-49	6	9
β-strand	55-57	3	8
β-strand	63-67	5	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-93	8	9
α-helix	95-97	3
β-strand	102-103	2	9
β-strand	107-111	5	9
β-strand	137-140	4	10
β-strand	143-147	5	9
β-strand	152-154	3	11
β-strand	155-158	4	10
β-strand	164-170	7	9
β-strand	177-183	7	9
β-strand	189-190	2	9
β-strand	198-201	4	11
β-strand	206	1	10
β-strand	207-211	5	11
α-helix	216-218	3
β-strand	220-229	10	9
β-strand	232-235	4	9
β-strand	239-244	6	9

Chain I: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	12
β-strand	9-12	4	13
α-helix	17	1
β-strand	18-20	3	14
β-strand	23-24	2	12
β-strand	31-37	7	13
β-strand	44-49	6	13
β-strand	55-57	3	14
α-helix	59-61	3
β-strand	62-65	4	14
β-strand	67	1	12
β-strand	72	1	12
β-strand	75-77	3	14
α-helix	82-84	3
β-strand	86-93	8	13
β-strand	102-103	2	13
β-strand	107-111	5	13
β-strand	137-140	4	15
β-strand	143-147	5	16
β-strand	152-154	3	17
β-strand	155-158	4	15
β-strand	164-170	7	16
β-strand	176-182	7	16
β-strand	189-190	2	16
β-strand	197-200	4	17
β-strand	206	1	15
β-strand	208-211	4	17
α-helix	216-218	3
β-strand	220-229	10	16
β-strand	232-235	4	16
β-strand	239-244	6	16

Chain K: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	18
β-strand	9-12	4	19
β-strand	18-20	3	20
β-strand	23-24	2	18
β-strand	31-37	7	19
β-strand	44-49	6	19
β-strand	55-57	3	20
β-strand	62-65	4	20
β-strand	67	1	18
β-strand	72	1	18
β-strand	75-77	3	20
α-helix	82-84	3
β-strand	86-93	8	19
β-strand	102-103	2	19
β-strand	107-111	5	19
β-strand	137-139	3	21
β-strand	144-147	4	22
β-strand	152-154	3	23
β-strand	156-158	3	21
β-strand	164-170	7	24
β-strand	176-182	7	24
β-strand	189-190	2	24
β-strand	198-200	3	23
β-strand	206	1	21
β-strand	208-211	4	23
β-strand	221-227	7	24
β-strand	233-235	3	24
β-strand	239-240	2	24
β-strand	241-244	4	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H2-Ld SBM2	A, E	protein	180	Mus musculus	P01897 (AlphaFold model)
QL9 peptide (QLSPFPFDL)	B, F	protein	9	Mus musculus	Q60597 (AlphaFold model)
42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)	C, G, I, K	protein	256	Mus musculus

Sequence of entity 1 (A, E), FASTA

>3TF7_1 H2-Ld SBM2 (chains A, E)
MGPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEY
WERITQVAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYD
GCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATL

Sequence of entity 2 (B, F), FASTA

>3TF7_2 QL9 peptide (QLSPFPFDL) (chains B, F)
QLSPFPFDL

Sequence of entity 3 (C, G, I, K), FASTA

>3TF7_3 42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain) (chains C, G, I, K)
MGAQSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGPQMLLKYYSGDPVVQ
GVNGFEAEFSKSDSSFHLRKASVHRSDSAVYFCAVSAKGTGSKLSFGKGAKLTVSPGGGG
SGGGGSGGGGSGGGGSEAAVTQSPRNKVTVTGENVTLSCRQTNSHNYMYWYRQDTGHELR
LIYYSYGAGNLQIGDVPDGYKATRTTQEDFFLTLESASPSQTSLYFCASSDAPGQLYFGE
GSKLTVLELEHHHHHH

Primary citation

T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex. Adams, J.J., Narayanan, S., Liu, B. et al. Immunity (2011) 35:681-693. DOI 10.1016/j.immuni.2011.09.013 · 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

Browse structure collections

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