3T8X: Human CD1b

Crystal structure of human CD1b in complex with synthetic antigenic diacylsulfoglycolipid SGL12 and endogenous spacer. Determined by X-ray diffraction at 1.9 Å resolution. Released 26 Oct 2011.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,803
Mol. weight: 96.73 kDa
Ligands: T8X, ULI
Released: 26 Oct 2011

Explore 3T8X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3T8X contains 23 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	35-41	7	1
β-strand	46-49	4	1
α-helix	60-84	25
β-strand	94-104	11	1
β-strand	110-118	9	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	135-137	3
α-helix	138-148	11
α-helix	154-160	7
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	2
α-helix	186-187	2
β-strand	188-193	6	3
β-strand	201-211	11	3
β-strand	212	1	2
β-strand	217-222	6	4
β-strand	225-226	2	4
β-strand	231-232	2	3
β-strand	236-238	3	3
β-strand	242-252	11	3
β-strand	259-264	6	4
α-helix	266-268	3
β-strand	273-276	4	4

Chains B and D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	8
β-strand	24-32	9	8
β-strand	35-41	7	8
β-strand	46-49	4	8
α-helix	60-84	25
α-helix	90-91	2
β-strand	94-104	11	8
α-helix	106-108	3
β-strand	110-118	9	8
β-strand	121-127	7	8
β-strand	130-133	4	8
α-helix	135-137	3
α-helix	138-148	11
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	9
β-strand	188-194	7	10
β-strand	201-211	11	10
β-strand	212	1	9
β-strand	217-222	6	11
β-strand	225-226	2	11
β-strand	231-232	2	10
β-strand	236-237	2	10
β-strand	243-252	10	10
β-strand	259-264	6	11
α-helix	266-268	3
β-strand	273-276	4	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1b	A, C	protein	301	Homo sapiens	P29016 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	99	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3T8X_1 T-cell surface glycoprotein CD1b (chains A, C)
EHAFQGPTSFHVIQTSSFTNSTWAQTQGSGWLDDLQIHGWDSDSGTAIFLKPWSKGNFSD
KEVAELEEIFRVYIFGFAREVQDFAGDFQMKYPFEIQGIAGCELHSGGAIVSFLRGALGG
LDFLSVKNASCVPSPEGGSRAQKFCALIIQYQGIMETVRILLYETCPRYLLGVLNAGKAD
LQRQVKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNAN
WTWYLRATLDVADGEAAGLSCRVKHSSLEGQDIILYWRNPIDKLGGGLNDIFEAQKIEWH
E

Sequence of entity 2 (B, D), FASTA

>3T8X_2 Beta-2-microglobulin (chains B, D)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
T8X	2-O-sulfo-alpha-D-glucopyranosyl 2-O-hexadecanoyl-3-O-[(2E,4S,6S,8S)-2,4,6,8-te…	C56 H104 O16 S	2
ULI	tetracontane	C40 H82	2

Water and common crystallization additives (SO4, ACT, GOL) are not listed.

Primary citation

Structural reorganization of the human CD1b Antigen-binding groove for presentation of mycobacterial sulfoglycolipids. Garcia-Alles, L.F., Collmann, A., Versluis, C. et al. To be published.

Other PDB entries of the same protein (UniProt P29016 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WL1 1.38 Å, Crystal Structure of Human CD1b in Complex with PG
8GLG 1.6 Å, Crystal Structure of Human CD1b in Complex with Phosphatidylethanolamine C34:1
5L2J 1.65 Å, Crystal Structure of human CD1b in complex with C36-GMM
5WKE 1.69 Å, Crystal Structure of Human CD1b in Complex with PS
6D64 1.7 Å, Crystal Structure of Human CD1b in Complex with POPC
7MX4 1.73 Å, CD1c with antigen analogue 1
2H26 1.8 Å, human CD1b in complex with endogenous phosphatidylcholine and spacer
8GLH 1.83 Å, Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5
9OI0 1.84 Å, Crystal structure of CD1b presenting ganglioside GD3
8GLE 1.85 Å, Crystal Structure of Human CD1b in Complex with Lysosulfatide
8DV3 1.9 Å, Crystal structure of human CD1b presenting Phosphatidylinositol C34:1
7MXF 2.0 Å, CD1c with antigen analogue 2

Browse structure collections

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