7M72: MHC-like protein complex structure

MHC-like protein complex structure. Determined by X-ray diffraction at 2.4 Å resolution. Released 10 Nov 2021.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 6,942
Mol. weight: 98.47 kDa
Ligands: HP6, QOD
Released: 10 Nov 2021

Explore 7M72 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M72 contains 25 α-helices and 72 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	24-32	9	1
β-strand	35-40	6	1
β-strand	48-49	2	1
α-helix	60-88	29
β-strand	96-107	12	1
β-strand	111-120	10	1
β-strand	123-129	7	1
β-strand	132-135	4	1
α-helix	136	1
α-helix	141-143	3
α-helix	144-152	9
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	190-197	8	3
β-strand	203-213	11	3
β-strand	214	1	2
β-strand	219-224	6	4
β-strand	227-228	2	4
α-helix	232	1
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
α-helix	282-289	8

Chain B: 3 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	35-41	7	7
β-strand	44-45	2	7
α-helix	46	1
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	78-84	7	7
β-strand	91-94	4	7

Chain C: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	9-13	5	9
β-strand	18-24	7	8
β-strand	31-37	7	9
β-strand	43-49	7	9
β-strand	53-58	6	8
β-strand	60-67	7	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-93	8	9
β-strand	104-106	3	9
β-strand	110-115	6	9
β-strand	124-129	6	10
β-strand	130	1	11
β-strand	137-142	6	10
α-helix	151-153	3
β-strand	158-160	3	10
β-strand	164-167	4	10
α-helix	169-171	3
β-strand	174-182	9	10
α-helix	189-191	3
β-strand	203	1	10

Chain D: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	31-37	7	13
β-strand	44-49	6	13
β-strand	56-57	2	13
β-strand	66-68	3	12
β-strand	74-79	6	12
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	102-103	2	13
β-strand	107-112	6	13
β-strand	119	1	14
α-helix	120-121	2
β-strand	122-126	5	11
α-helix	127-129	3
α-helix	130-136	7
β-strand	138-148	11	11
β-strand	149	1	14
β-strand	153-159	7	15
β-strand	162-164	3	15
β-strand	168-170	3	11
α-helix	174	1
β-strand	175-176	2	11
β-strand	186-195	10	11
α-helix	196-199	4
β-strand	205-212	8	15
β-strand	215	1	16
α-helix	226-227	2
β-strand	229	1	16
β-strand	231-238	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d1	A	protein	302	Mus musculus	P11609 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Mus musculus	P01887 (AlphaFold model)
NKT Valpha14 (Mouse)-2C12 TCR,Human T-cell receptor sp3.4 alpha chain	C	protein	207	Mus musculus, Homo sapiens	K7N5N2 (AlphaFold model)
NKT Vbeta8.2 (Mouse)-2C12 TCR,Human nkt tcr beta chain	D	protein	242	Mus musculus, Homo sapiens	K7N5M4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7M72_1 Antigen-presenting glycoprotein CD1d1 (chains A)
SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSN
QQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAF
QGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGK
SDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN
ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHHH
HH

Sequence of entity 2 (B), FASTA

>7M72_2 Beta-2-microglobulin (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (C), FASTA

>7M72_3 NKT Valpha14 (Mouse)-2C12 TCR,Human T-cell receptor sp3.4 alpha chain (chains C)
TQVEQSPQSLVVRQGENSVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGR
YSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>7M72_4 NKT Vbeta8.2 (Mouse)-2C12 TCR,Human nkt tcr beta chain (chains D)
MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGD
IPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

ID	Name	Formula	Copies
HP6	Heptane	C7 H16	1
QOD	(3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxy-15-methylhexadecan-2-…	C40 H79 N O9	1

Primary citation

Host immunomodulatory lipids created by symbionts from dietary amino acids. Oh, S.F., Praveena, T., Song, H. et al. Nature (2021) 600:302-307. DOI 10.1038/s41586-021-04083-0 · 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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