2AKR: Sulfatide presentation by mouse CD1d

Structural basis of sulfatide presentation by mouse CD1d. Determined by X-ray diffraction at 1.9 Å resolution. Released 6 Dec 2005.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,918
Mol. weight: 91.9 kDa
Ligands: NAG, CIS
Released: 6 Dec 2005

Explore 2AKR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2AKR contains 20 α-helices and 60 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-20	12	1
β-strand	23-32	10	1
β-strand	35-40	6	1
α-helix	47	1
β-strand	48-49	2	1
α-helix	60-86	27
β-strand	96-105	10	1
β-strand	113-120	8	1
β-strand	123-129	7	1
β-strand	132-135	4	1
α-helix	141-143	3
α-helix	144-150	7
α-helix	154-162	9
α-helix	163-167	5
α-helix	168-178	11
α-helix	180-183	4
β-strand	187	1	2
β-strand	190-196	7	3
β-strand	203-213	11	3
β-strand	214	1	2
β-strand	219-224	6	4
β-strand	227-228	2	4
β-strand	233-234	2	3
β-strand	238-239	2	3
β-strand	245-254	10	3
β-strand	262-266	5	4
α-helix	268-270	3
β-strand	275-278	4	4

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	8
β-strand	24-32	9	8
β-strand	35-40	6	8
β-strand	48-49	2	8
α-helix	60-84	25
β-strand	96-105	10	8
β-strand	113-120	8	8
β-strand	123-129	7	8
β-strand	132-135	4	8
α-helix	141-143	3
α-helix	144-150	7
α-helix	154-162	9
α-helix	163-167	5
α-helix	168-178	11
α-helix	180-183	4
β-strand	187	1	9
β-strand	190-196	7	10
β-strand	203-213	11	10
β-strand	214	1	9
β-strand	219-224	6	11
β-strand	227-228	2	11
β-strand	233-234	2	10
β-strand	238-239	2	10
β-strand	245-254	10	10
β-strand	261-266	6	11
α-helix	268-270	3
β-strand	275-278	4	11

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1d1	A, C	protein	285	Mus musculus	P11609 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	99	Mus musculus	P01887 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2AKR_1 T-cell surface glycoprotein CD1d1 (chains A, C)
SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSN
QQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAF
QGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGK
SDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN
ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWHHHHHH

Sequence of entity 2 (B, D), FASTA

>2AKR_2 Beta-2-microglobulin (chains B, D)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
CIS	(15Z)-N-((1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl…	C48 H91 N O11 S	2

Primary citation

Structural basis for CD1d presentation of a sulfatide derived from myelin and its implications for autoimmunity. Zajonc, D.M., Maricic, I., Wu, D. et al. J Exp Med (2005) 202:1517-1526. DOI 10.1084/jem.20051625 · PubMed

Other PDB entries of the same protein (UniProt P11609 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
6C6F 1.67 Å, Structure of glycolipid aGSA[26,P5p] in complex with mouse CD1d
3GML 1.7 Å, Structure of mouse CD1d in complex with C6Ph
3GMN 1.7 Å, Structure of mouse CD1d in complex with C10Ph
3GMP 1.7 Å, Structure of mouse CD1d in complex with PBS-25
3T1F 1.7 Å, Crystal structure of the mouse CD1d-Glc-DAG-s2 complex
5TW2 1.75 Å, Structure of mouse CD1d with bound alpha-galactosylsphingamide JG168
6C6J 1.79 Å, Structure of glycolipid aGSA[8,P5p] in complex with mouse CD1d
2FIK 1.8 Å, Structure of a microbial glycosphingolipid bound to mouse CD1d
3GMM 1.8 Å, Structure of mouse CD1d in complex with C8Ph
3GMQ 1.8 Å, Structure of mouse CD1d expressed in SF9 cells, no ligand added

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