4X6D: T-cell surface glycoprotein CD1a

CD1a ternary complex with endogenous lipids and BK6 TCR. Determined by X-ray diffraction at 2.98 Å resolution. Released 28 Jan 2015.

Method: X-ray diffraction
Resolution: 2.98 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,304
Mol. weight: 189.5 kDa
Ligands: OLA, PAM
Released: 28 Jan 2015

Explore 4X6D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4X6D contains 41 α-helices and 138 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: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-17	10	1
β-strand	26-32	7	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	52-54	3
α-helix	60-82	23
β-strand	95-104	10	1
β-strand	109-118	10	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	152-160	9
α-helix	161-165	5
α-helix	166-176	11
β-strand	185	1	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	228	1	5
β-strand	230	1	5
β-strand	231-232	2	3
β-strand	236-237	2	3
β-strand	243-252	10	3
α-helix	253-255	3
β-strand	260-264	5	4
α-helix	266-268	3
β-strand	273-276	4	4

Chain B: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	35-37	3	8
β-strand	50-51	2	7
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	80-84	5	8
β-strand	91-93	3	8

Chain C: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	9
β-strand	25-32	8	9
β-strand	35-39	5	9
α-helix	47	1
β-strand	48-49	2	9
α-helix	60-81	22
α-helix	86-88	3
β-strand	94-105	12	9
β-strand	108-118	11	9
β-strand	122-127	6	9
β-strand	130-133	4	9
α-helix	138-148	11
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-177	12
β-strand	185	1	10
β-strand	207-211	5	11
β-strand	212	1	10
β-strand	232-237	6	11
β-strand	243-247	5	11

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
β-strand	6-10	5	13
β-strand	23-30	8	13
β-strand	31	1	12
β-strand	36-39	4	14
β-strand	40-41	2	15
β-strand	44-45	2	15
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-68	7	13
β-strand	80-83	4	14
β-strand	91-93	3	14

Chain E: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	16
β-strand	10-13	4	17
β-strand	18-24	7	16
β-strand	29-37	9	17
β-strand	43-50	8	17
β-strand	53-57	5	16
β-strand	60-65	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-92	9	17
β-strand	101-102	2	17
β-strand	106-111	6	17
β-strand	120-124	5	18
β-strand	134-138	5	18
β-strand	155-156	2	18
α-helix	157-159	3
β-strand	160-164	5	18
α-helix	165-167	3
β-strand	169-177	9	18
α-helix	185-187	3
β-strand	199	1	18

Chain F: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-14	5	20
β-strand	19-25	7	19
β-strand	31-37	7	20
β-strand	43-51	9	20
β-strand	54-57	4	20
β-strand	64-67	4	19
β-strand	73-78	6	19
α-helix	83-85	3
β-strand	87-94	8	20
β-strand	105-106	2	20
β-strand	110-115	6	20
α-helix	118-120	3
β-strand	122	1	21
β-strand	125-129	5	22
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	22
β-strand	152	1	21
β-strand	156-162	7	23
β-strand	165-167	3	23
β-strand	171-173	3	22
α-helix	177	1
β-strand	178-179	2	22
β-strand	189-198	10	22
α-helix	199-202	4
β-strand	208-215	8	23
β-strand	218	1	24
α-helix	229-230	2
β-strand	232	1	24
β-strand	234-241	8	23

Chain G: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	25
β-strand	10-13	4	26
β-strand	18-24	7	25
β-strand	29-37	9	26
β-strand	44-50	7	26
β-strand	53-57	5	25
β-strand	60-65	6	25
β-strand	70-75	6	25
α-helix	80-82	3
β-strand	84-92	9	26
β-strand	101-102	2	26
β-strand	106-111	6	26
α-helix	112-113	2
β-strand	120-126	7	27
β-strand	133-138	6	27
β-strand	155-156	2	27
α-helix	157-159	3
β-strand	160-164	5	27
α-helix	165-167	3
β-strand	169-177	9	27
α-helix	185-187	3
β-strand	199	1	27

Chain H: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-14	5	29
β-strand	19-25	7	28
β-strand	31-37	7	29
β-strand	43-51	9	29
β-strand	54-57	4	29
β-strand	64-67	4	28
β-strand	73-78	6	28
α-helix	83-85	3
β-strand	87-94	8	29
β-strand	105-106	2	29
β-strand	110-115	6	29
α-helix	118-120	3
β-strand	122	1	30
β-strand	125-130	6	27
α-helix	131-132	2
α-helix	133-139	7
β-strand	141-151	11	27
β-strand	152	1	30
β-strand	156-162	7	31
β-strand	165-167	3	31
β-strand	171-173	3	27
α-helix	177	1
β-strand	178-179	2	27
β-strand	189-198	10	27
α-helix	199-202	4
β-strand	208-215	8	31
β-strand	218	1	32
α-helix	229-230	2
β-strand	232	1	32
β-strand	234-241	8	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1a	A, C	protein	275	Homo sapiens	P06126 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	99	Homo sapiens	P61769 (AlphaFold model)
TCR alpha	E, G	protein	207	Homo sapiens	P01848 (AlphaFold model)
TCR beta	F, H	protein	245	Homo sapiens	P01850 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4X6D_1 T-cell surface glycoprotein CD1a (chains A, C)
LKEPLSFHVIWIASFYNHSWKQNLVSGWLSDLQTHTWDSNSSTIVFLWPWSRGNFSNEEW
KELETLFRIRTIRSFEGIRRYAHELQFEYPFEIQVTGGCELHSGKVSGSFLQLAYQGSDF
VSFQNNSWLPYPVAGNMAKHFCKVLNQNQHENDITHNLLSDTCPRFILGLLDAGKAHLQR
QVKPEAWLSHGPSPGPGHLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQRGDILPSADGTW
YLRATLEVAAGEAADLSCRVKHSSLEGQDIVLYWE

Sequence of entity 2 (B, D), FASTA

>4X6D_2 Beta-2-microglobulin (chains B, D)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, G), FASTA

>4X6D_3 TCR alpha (chains E, G)
QKEVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQYSRKGPELLMYTYSSGNKEDGR
FTAQVDKSSKYISLFIRDSQPSDSATYLCAMSTSLPNAGKSTFGDGTTLTVKPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>4X6D_4 TCR beta (chains F, H)
NAGVTQTPKFRVLKTGQSMTLLCAQDMNHEYMYWYRQDPGMGLRLIHYSVGEGTTAKGEV
PDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASRYFLPTQGMGAFFGQGTRLTVVEDLNK
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
OLA	Oleic acid	C18 H34 O2	1
PAM	Palmitoleic acid	C16 H30 O2	1

Primary citation

alpha beta T cell antigen receptor recognition of CD1a presenting self lipid ligands. Birkinshaw, R.W., Pellicci, D.G., Cheng, T.Y. et al. Nat Immunol (2015) 16:258-266. DOI 10.1038/ni.3098 · PubMed

Other PDB entries of the same protein (UniProt P06126 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5J1A 1.86 Å, Antigen presenting molecule
4X6F 1.91 Å, CD1a binary complex with sphingomyelin
7SH4 2.0 Å, CD1a-phosphatidylglycerol binary structure
7KP1 2.02 Å, CD1a-42:2 SM binary complex
4X6E 2.1 Å, CD1a binary complex with lysophosphatidylcholine
9OHZ 2.14 Å, Crystal structure of CD1a presenting ganglioside GD3
1ONQ 2.15 Å, Crystal Structure of CD1a in Complex with a Sulfatide
6NUX 2.2 Å, CD1a-lipid binary complex
7KOZ 2.25 Å, CD1a-36:2 SM binary complex
7KP0 2.4 Å, CD1a-42:1 SM binary complex
7RYN 2.7 Å, CD1a-sulfatide-gdTCR complex
1XZ0 2.8 Å, Crystal structure of CD1a in complex with a synthetic mycobactin lipopeptide

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