4MNH: DP10.7 TCR

Structure of the DP10.7 TCR. Determined by X-ray diffraction at 3.3 Å resolution. Released 18 Dec 2013.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,440
Mol. weight: 109.37 kDa
Released: 18 Dec 2013

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

Secondary structure: helices and β-sheets

4MNH contains 25 α-helices and 83 β-strands across 4 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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	10-14	5	1
β-strand	19-22	4	2
β-strand	32-38	7	1
β-strand	45-51	7	1
β-strand	57-59	3	1
α-helix	63-64	2
β-strand	68-71	4	2
β-strand	79-82	4	2
α-helix	87-89	3
β-strand	91-98	8	1
β-strand	105-107	3	1
β-strand	111-116	6	1
α-helix	119-121	3
β-strand	123	1	3
β-strand	126-130	5	4
α-helix	131-133	3
α-helix	134-139	6
β-strand	142-152	11	4
β-strand	153	1	3
β-strand	157-163	7	5
β-strand	166-167	2	5
β-strand	172-174	3	4
α-helix	178	1
β-strand	179-180	2	4
β-strand	190-199	10	4
α-helix	200-203	4
β-strand	209-216	8	5
β-strand	219	1	6
α-helix	230-231	2
β-strand	233	1	6
β-strand	235-242	8	5

Chain B: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	10-14	5	8
β-strand	19-21	3	7
β-strand	24	1	7
β-strand	33-39	7	8
β-strand	45-52	8	8
α-helix	56-58	3
β-strand	59-60	2	7
β-strand	63-68	6	7
β-strand	73-78	6	7
α-helix	83-85	3
β-strand	87-94	8	8
β-strand	107-109	3	8
β-strand	113-118	6	8
α-helix	119	1
β-strand	127-130	4	9
β-strand	133	1	4
β-strand	142-145	4	9
β-strand	162-163	2	9
α-helix	164-166	3
β-strand	167-171	5	9
β-strand	176-184	9	9

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	9-14	6	10
β-strand	19-23	5	11
β-strand	32-38	7	10
β-strand	45-51	7	10
β-strand	57-59	3	10
α-helix	63-64	2
β-strand	68-71	4	11
β-strand	78-82	5	11
α-helix	87-89	3
β-strand	91-98	8	10
β-strand	105-107	3	10
β-strand	111-116	6	10
α-helix	119-121	3
β-strand	123	1	12
β-strand	126-130	5	13
α-helix	131-133	3
α-helix	134-139	6
β-strand	142-152	11	13
β-strand	153	1	12
β-strand	157-163	7	14
β-strand	166-167	2	14
β-strand	172-174	3	13
α-helix	178	1
β-strand	179-180	2	13
β-strand	190-199	10	13
α-helix	200-203	4
β-strand	209-216	8	14
β-strand	219	1	15
α-helix	230-231	2
β-strand	233	1	15
β-strand	235-242	8	14

Chain D: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	16
β-strand	10-13	4	17
β-strand	19-21	3	16
β-strand	24	1	16
β-strand	33-39	7	17
β-strand	45-52	8	17
α-helix	56-58	3
β-strand	59-60	2	16
β-strand	63-68	6	16
β-strand	73-78	6	16
α-helix	83-85	3
β-strand	87-94	8	17
α-helix	102-104	3
β-strand	107-109	3	17
β-strand	113-117	5	17
β-strand	127-132	6	18
β-strand	133	1	13
β-strand	140-145	6	18
β-strand	161-163	3	18
α-helix	164-166	3
β-strand	167-170	4	18
β-strand	177-185	9	18
β-strand	206	1	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell receptor gamma chain V region PT-gamma-1/2, Human nkt tcr beta chain	A, C	protein	259	Homo sapiens	K7N5M4 (AlphaFold model)
Human nkt tcr alpha chain	B, D	protein	226	Homo sapiens	Q6PJ56 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4MNH_1 T-cell receptor gamma chain V region PT-gamma-1/2, Human nkt tcr beta chain (chains A, C)
PDLSSNLEGRTKSVIRQTGSSAEITCDLAEGSTGYIHWYLHQEGKAPQRLLYYDSYTSSV
VLESGISPGKYDTYGSTRKNLRMILRNLIENDSGVYYCATWDEKYYKKLFGSGTTLVVTE
DLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQ
PLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIV
SAEAWGRADSRGGLEVLFQ

Sequence of entity 2 (B, D), FASTA

>4MNH_2 Human nkt tcr alpha chain (chains B, D)
ADPAQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQN
AKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGEPSYWGFPRTTRVIFGKGTRVTV
EPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFK
SNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSSRGGLEVLFQ

Primary citation

Crystal Structure of V delta 1 T Cell Receptor in Complex with CD1d-Sulfatide Shows MHC-like Recognition of a Self-Lipid by Human gamma delta T Cells. Luoma, A.M., Castro, C.D., Mayassi, T. et al. Immunity (2013) 39:1032-1042. DOI 10.1016/j.immuni.2013.11.001 · PubMed

Other PDB entries of the same protein (UniProt K7N5M4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6AT6 1.42 Å, Crystal structure of the KFJ5 TCR
6BJ8 1.75 Å, TCR55 in complex with Pep20/HLA-B35
6U07 1.76 Å, Computational Stabilization of T Cell Receptor Constant Domains
7N4K 1.85 Å, 6218 TCR in complex with H2-Db PA 224
7N5C 1.87 Å, 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond
6BJ3 1.9 Å, TCR55 in complex with HIV(Pol448-456)/HLA-B35
7N5P 2.09 Å, 6218 TCR in complex with H2-Db PA224-233 with a cysteine mutant
5WLG 2.1 Å, Crystal Structure of H-2Db with the GAP501 peptide (SQL)
6R2L 2.3 Å, NYBR1-A2-slskildtv
6D78 2.35 Å, The complex between high-affinity TCR DMF5(alpha-D26Y,beta-L98W) and human Class I MHC…
7M72 2.4 Å, MHC-like protein complex structure
6Q3S 2.5 Å, Engineered Human HLA_A2 MHC Class I molecule in complex with TCR and SV9 peptide

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