2DYP: LILRB2(LIR2/ILT4/CD85d)

Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G. Determined by X-ray diffraction at 2.5 Å resolution. Released 7 Nov 2006.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,696
Mol. weight: 66.94 kDa
Released: 7 Nov 2006

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

Secondary structure: helices and β-sheets

2DYP contains 15 α-helices and 52 β-strands across 3 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	4-12	9	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-53	4
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	153-161	9
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-194	9	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	223	1	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	3	1	6
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-46	3	8
β-strand	50-51	2	7
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
β-strand	91-94	4	8

Chain D: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	7-11	5	9
β-strand	15-17	3	10
β-strand	22-27	6	9
β-strand	34-39	6	11
α-helix	55-57	3
β-strand	59-62	4	9
α-helix	67-69	3
β-strand	71-79	9	11
β-strand	82-83	2	11
α-helix	85-89	5
β-strand	90-92	3	11
β-strand	93-95	3	10
β-strand	102-106	5	12
β-strand	110	1	13
β-strand	115-122	8	12
β-strand	125	1	5
β-strand	129-134	6	14
β-strand	142-145	4	14
β-strand	155-163	9	12
β-strand	170-176	7	14
β-strand	183	1	10
β-strand	184	1	14
α-helix	186-190	5
β-strand	191-192	2	14
β-strand	194	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain G	A	protein	277	Homo sapiens	P17693 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
9 Mer Peptide From Histone H2A.x	C	protein	9		P16104 (AlphaFold model)
Leukocyte immunoglobulin-like receptor subfamily B member 2	D	protein	196	Homo sapiens	Q8N423 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2DYP_1 HLA class I histocompatibility antigen, alpha chain G (chains A)
MGSHSMRYFSAAVSRPGRGEPRFIAMGYVDDTQFVRFDSDSASPRMEPRAPWVEQEGPEY
WEEETRNTKAHAQTDRMNLQTLRGYYNQSEASSHTLQWMIGCDLGSDGRLLRGYEQYAYD
GKDYLALNEDLRSWTAADTAAQISKRKCEAANVAEQRRAYLEGTCVEWLHRYLENGKEML
QRADPPKTHVTHHPVFDYEATLRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLMLRWKQ

Sequence of entity 2 (B), FASTA

>2DYP_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>2DYP_3 9 Mer Peptide From Histone H2A.x (chains C)
RIIPRHLQL

Sequence of entity 4 (D), FASTA

>2DYP_4 Leukocyte immunoglobulin-like receptor subfamily B member 2 (chains D)
GTIPKPTLWAEPDSVITQGSPVTLSCQGSLEAQEYRLYREKKSASWITRIRPELVKNGQF
RIPSITWEHTGRYGCQYYSRARWSELSDPLVLVMTGAYPKPTLSAQPSPVVTSGGRVTLQ
CESQVAFGGFILCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPNRRWSHRCYGYDLNS
PYVWSSPSDLLELLVP

Primary citation

Structural basis for recognition of the nonclassical MHC molecule HLA-G by the leukocyte Ig-like receptor B2 (LILRB2/LIR2/ILT4/CD85d). Shiroishi, M., Kuroki, K., Rasubala, L. et al. Proc Natl Acad Sci U S A (2006) 103:16412-16417. DOI 10.1073/pnas.0605228103 · PubMed

Other PDB entries of the same protein (UniProt P17693 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KYO 1.7 Å, Crystal structure of HLA-G presenting KLPAQFYIL peptide
1YDP 1.9 Å, 1.9A crystal structure of HLA-G
3KYN 2.4 Å, Crystal structure of HLA-G presenting KGPPAALTL peptide
3BZE 2.5 Å, The human non-classical major histocompatibility complex molecule HLA-E
6K60 3.15 Å, Structural and functional basis for HLA-G isoform recognition of immune checkpoint…
2D31 3.2 Å, Crystal structure of disulfide-linked HLA-G dimer
6AEE 3.3 Å, Crystal structure of the four Ig-like domains of LILRB1 complexed with HLA-G
3CDG 3.4 Å, Human CD94/NKG2A in complex with HLA-E
9RWI 3.45 Å, crystal structure of a human leukocyte antigen-A (HLA-G) blocking antibody
3CII 4.41 Å, Structure of NKG2A/CD94 bound to HLA-E

Browse structure collections

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