1YDP: 1.9A crystal structure of HLA-G

1.9A crystal structure of HLA-G. Determined by X-ray diffraction at 1.9 Å resolution. Released 8 Mar 2005.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 3,590
Mol. weight: 45.02 kDa
Ligands: CO
Released: 8 Mar 2005

Explore 1YDP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YDP contains 13 α-helices and 30 β-strands across 2 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	50-52	3
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	138-150	13
α-helix	153-158	6
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-192	7	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	223	1	4
α-helix	225-227	3
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: 1 helix, 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
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	275	Homo sapiens	P17693 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
histone 2a peptide	P	protein	9	synthetic construct	P16104 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1YDP_1 MHC class I antigen (chains A)
SHSMRYFSAAVSRPGRGEPRFIAMGYVDDTQFVRFDSDSASPRMEPRAPWVEQEGPEYWE
EETRNTKAHAQTDRMNLQTLRGYYNQSEASSHTLQWMIGCDLGSDGRLIRGYERYAYDGK
DYLALNEDLRSWTAADTAAQISKRKCEAANVAEQRRAYLEGTCVEWLHRYLENGKEMLQR
ADPPKTHVTHHPVFDYEATLRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAGDGTF
QKWAAVVVPSGEEQRYTCHVQHEGLPEPLMLRWKQ

Sequence of entity 2 (B), FASTA

>1YDP_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (P), FASTA

>1YDP_3 histone 2a peptide (chains P)
RIIPRHLQL

Ligands and cofactors

ID	Name	Formula	Copies
CO	Cobalt (II) ion	Co	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Crystal structure of HLA-G: A nonclassical MHC class I molecule expressed at the fetal-maternal interface. Clements, C.S., Kjer-Nielsen, L., Kostenko, L. et al. Proc Natl Acad Sci U S A (2005) 102:3360-3365. DOI 10.1073/pnas.0409676102 · 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
3KYN 2.4 Å, Crystal structure of HLA-G presenting KGPPAALTL peptide
2DYP 2.5 Å, Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G
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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