4MNG: DP10.7 TCR with CD1d-sulfatide

Structure of the DP10.7 TCR with CD1d-sulfatide. Determined by X-ray diffraction at 3.01 Å resolution. Released 18 Dec 2013.

Method: X-ray diffraction
Resolution: 3.01 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 9,775
Mol. weight: 147.44 kDa
Ligands: CIS, NAG
Released: 18 Dec 2013

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

Secondary structure: helices and β-sheets

4MNG contains 37 α-helices and 108 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	4
β-strand	24-32	9	4
β-strand	35-40	6	4
β-strand	47-49	3	4
α-helix	60-87	28
α-helix	90-91	2
α-helix	93	1
β-strand	94-104	11	4
β-strand	110-118	9	4
β-strand	121-127	7	4
β-strand	130-133	4	4
α-helix	141-149	9
α-helix	152-159	8
α-helix	160-165	6
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	5
β-strand	188-195	8	6
β-strand	201-211	11	6
β-strand	212	1	5
β-strand	217-222	6	7
β-strand	225-226	2	7
α-helix	227	1
β-strand	231-232	2	6
β-strand	236-237	2	6
β-strand	243-252	10	6
β-strand	259-264	6	7
α-helix	266-268	3
β-strand	273-276	4	7

Chains B and D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3	1	1
α-helix	4-5	2
β-strand	6-11	6	2
β-strand	21-30	10	2
β-strand	31	1	1
β-strand	35-41	7	3
β-strand	44-45	2	3
β-strand	50-51	2	2
α-helix	52-54	3
β-strand	55-56	2	2
β-strand	62-70	9	2
β-strand	78-84	7	3
β-strand	91-94	4	3

Chain C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	11
β-strand	24-32	9	11
β-strand	35-40	6	11
β-strand	47-49	3	11
α-helix	60-87	28
α-helix	90-91	2
α-helix	93	1
β-strand	94-104	11	11
β-strand	110-118	9	11
β-strand	121-127	7	11
β-strand	130-133	4	11
α-helix	141-149	9
α-helix	152-159	8
α-helix	160-165	6
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	12
β-strand	188-195	8	13
β-strand	202-211	10	13
β-strand	212	1	12
β-strand	217-222	6	14
β-strand	225-226	2	14
α-helix	227	1
β-strand	231-232	2	13
β-strand	236-237	2	13
β-strand	243-251	9	13
β-strand	259-264	6	14
α-helix	266-268	3
β-strand	273-276	4	14

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	15
β-strand	10-14	5	16
β-strand	19-21	3	15
β-strand	24-25	2	15
β-strand	33-39	7	16
β-strand	45-52	8	16
β-strand	59-60	2	15
β-strand	63-68	6	15
β-strand	73-78	6	15
α-helix	83-85	3
β-strand	87-94	8	16
β-strand	97	1	17
β-strand	100	1	17
β-strand	107-109	3	16
α-helix	110	1
β-strand	113-118	6	16
β-strand	148-153	6	18
β-strand	158-161	4	19
β-strand	171-177	7	18
β-strand	184-190	7	18
β-strand	195-198	4	18
α-helix	199	1
α-helix	202-203	2
β-strand	207-210	4	19
β-strand	218-221	4	19
α-helix	226-228	3
β-strand	230-237	8	18
β-strand	244-246	3	18
β-strand	250-255	6	18

Chain F: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	20
β-strand	10-14	5	21
β-strand	19-21	3	20
β-strand	24-25	2	20
β-strand	33-39	7	21
β-strand	45-52	8	21
α-helix	56-58	3
β-strand	59-60	2	20
β-strand	63-68	6	20
β-strand	73-78	6	20
α-helix	83-85	3
β-strand	87-94	8	21
β-strand	97	1	22
β-strand	100	1	22
β-strand	107-109	3	21
α-helix	110	1
β-strand	113-118	6	21
β-strand	148-153	6	23
β-strand	158-161	4	24
β-strand	171-177	7	23
β-strand	184-190	7	23
β-strand	195-198	4	23
α-helix	199	1
α-helix	202-203	2
β-strand	207-210	4	24
β-strand	218-221	4	24
α-helix	226-228	3
β-strand	230-237	8	23
β-strand	244-246	3	23
β-strand	250-255	6	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin	B, D	protein	99	Mus musculus	P01887 (AlphaFold model)
Cd1d1 protein	A, C	protein	281	Mus musculus	P11609 (AlphaFold model), P15813 (AlphaFold model)
TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region	E, F	protein	262	Homo sapiens	Q6PJ56 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>4MNG_1 Beta-2-microglobulin (chains B, D)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 2 (A, C), FASTA

>4MNG_2 Cd1d1 protein (chains A, C)
ADPVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFS
DQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQ
GKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKS
ELKKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNA
DETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWSGR

Sequence of entity 3 (E, F), FASTA

>4MNG_3 TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region (chains E, F)
AQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKS
GRYSVNFKKAAKSVALTISALQLEDSAKYFCALGEPSYWGFPRTTRVIFGKGTRVTVEPG
GGGSGGGGSGGGGSGGGGSSSNLEGRTKSVIRQTGSSAEITCDLAEGSTGYIHWYLHQEG
KAPQRLLYYDSYTSSVVLESGISPGKYDTYGSTRKNLRMILRNLIENDSGVYYCATWDEK
YYKKLFGSGTKLIITDAASGAD

Ligands and cofactors

ID	Name	Formula	Copies
CIS	(15Z)-N-((1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl…	C48 H91 N O11 S	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

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 P01887 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LK2 1.35 Å, 1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide
1G7P 1.5 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
1KPU 1.5 Å, High resolution crystal structure of the MHC class I complex H-2Kb/VSV8
5WEU 1.58 Å, Crystal Structure of H2-Dd with disulfide-linked 10mer peptide
1G7Q 1.6 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
3G08 1.6 Å, Crystal structure of the alpha-galactosylceramide analog OCH in complex with mouse CD1d
3GMO 1.6 Å, Structure of mouse CD1d in complex with C8PhF
7LFK 1.6 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, thr mutant, refined…
7LFL 1.6 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, val mutant,…
7LFM 1.6 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, val mutant,…
6C6F 1.67 Å, Structure of glycolipid aGSA[26,P5p] in complex with mouse CD1d
3ECB 1.7 Å, Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human…

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