6AEE: Four Ig-like domains of LILRB1

Crystal structure of the four Ig-like domains of LILRB1 complexed with HLA-G. Determined by X-ray diffraction at 3.3 Å resolution. Released 31 Jul 2019.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,038
Mol. weight: 178.43 kDa
Released: 31 Jul 2019

Explore 6AEE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AEE contains 39 α-helices and 139 β-strands across 7 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	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	122-126	5	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	186-195	10	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	228-230	3	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	253-256	4
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 1 helix, 13 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	35-41	7	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	7
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-84	7	8
β-strand	87	1	9
β-strand	91-94	4	8

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Chain D: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	10
α-helix	20	1
β-strand	21-28	8	10
β-strand	31-37	7	10
β-strand	46-47	2	10
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	10
β-strand	109-118	10	10
β-strand	122-126	5	10
β-strand	133-135	3	10
α-helix	140-150	11
α-helix	153-158	6
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	11
α-helix	184-185	2
β-strand	186	1	12
β-strand	189-195	7	12
β-strand	198-208	11	12
β-strand	209	1	11
β-strand	214-219	6	13
β-strand	223	1	13
β-strand	228-230	3	12
β-strand	234-235	2	12
β-strand	241-250	10	12
α-helix	254-256	3
β-strand	257-262	6	13
β-strand	270-272	3	13

Chain E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	14
α-helix	4-5	2
β-strand	6-11	6	15
β-strand	21-30	10	15
β-strand	31	1	14
β-strand	35-41	7	16
β-strand	44-45	2	16
α-helix	46	1
β-strand	50-51	2	15
β-strand	55-56	2	15
β-strand	62-70	9	15
β-strand	78-84	7	16
β-strand	87	1	17
β-strand	91-94	4	16

Chain G: 6 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	18
β-strand	15-17	3	19
β-strand	22-27	6	18
β-strand	35-39	5	20
α-helix	47-49	3
α-helix	52-55	4
β-strand	59-62	4	18
β-strand	71-77	7	20
α-helix	84-90	7
β-strand	91-93	3	20
β-strand	94-96	3	19
β-strand	99	1	9
β-strand	103-107	5	21
β-strand	119-123	5	21
β-strand	126	1	5
β-strand	130-136	7	22
α-helix	141-142	2
β-strand	143	1	22
β-strand	146	1	22
β-strand	156-160	5	21
β-strand	171-177	7	22
β-strand	184	1	19
β-strand	185	1	22
α-helix	187-191	5
β-strand	192-193	2	22
β-strand	204-208	5	23
β-strand	212-213	2	24
β-strand	219-224	6	23
β-strand	231-236	6	25
β-strand	244-247	4	25
β-strand	257-261	5	23
β-strand	270-277	8	25
β-strand	291-293	3	25
β-strand	294-295	2	24
β-strand	303-307	5	26
β-strand	318-325	8	26
β-strand	331-336	6	27
β-strand	346-347	2	27
β-strand	349-351	3	26
β-strand	354-363	10	26
β-strand	371-377	7	27
β-strand	384	1	24
α-helix	387-391	5
β-strand	392-393	2	27

Chain H: 9 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	28
β-strand	15-17	3	29
β-strand	22-27	6	28
β-strand	36-39	4	30
α-helix	45-47	3
α-helix	52-57	6
β-strand	59-62	4	28
α-helix	67-69	3
β-strand	71-76	6	30
α-helix	86-90	5
β-strand	91-93	3	30
β-strand	94-96	3	29
β-strand	99	1	17
α-helix	100-102	3
β-strand	103-107	5	31
β-strand	119-123	5	31
β-strand	130-135	6	32
β-strand	145	1	32
β-strand	156-160	5	31
β-strand	171-177	7	32
β-strand	184	1	29
α-helix	187-191	5
β-strand	192-193	2	32
β-strand	204-208	5	33
β-strand	219	1	34
β-strand	220-224	5	33
β-strand	231-236	6	35
β-strand	245-247	3	35
β-strand	257-258	2	33
β-strand	261	1	34
α-helix	266-268	3
β-strand	270-277	8	35
α-helix	286-290	5
β-strand	291-293	3	35
β-strand	295	1	36
β-strand	303-306	4	37
β-strand	318-325	8	37
β-strand	331-336	6	38
β-strand	345-347	3	38
β-strand	349-351	3	37
β-strand	354-363	10	37
β-strand	370-377	8	38
β-strand	384	1	36
β-strand	385	1	38
α-helix	387-391	5
β-strand	392-394	3	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain G	A, D	protein	277	Homo sapiens	P17693 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	100	Homo sapiens	P61769 (AlphaFold model)
9 Mer Peptide (RL9) From Histone H2A.x	C, F	protein	9	Homo sapiens	P04908 (AlphaFold model)
Leukocyte immunoglobulin-like receptor subfamily B member 1	G, H	protein	399	Homo sapiens	Q8NHL6 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6AEE_1 HLA class I histocompatibility antigen, alpha chain G (chains A, D)
MGSHSMRYFSAAVSRPGRGEPRFIAMGYVDDTQFVRFDSDSASPRMEPRAPWVEQEGPEY
WEEETRNTKAHAQTDRMNLQTLRGYYNQSEASSHTLQWMIGCDLGSDGRLIRGYERYAYD
GKDYLALNEDLRSWTAADTAAQISKRKCEAANVAEQRRAYLEGTCVEWLHRYLENGKEML
QRADPPKTHVTHHPVFDYEATLRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLMLRWKQ

Sequence of entity 2 (B, E), FASTA

>6AEE_2 Beta-2-microglobulin (chains B, E)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F), FASTA

>6AEE_3 9 Mer Peptide (RL9) From Histone H2A.x (chains C, F)
RIIPRHLQL

Sequence of entity 4 (G, H), FASTA

>6AEE_4 Leukocyte immunoglobulin-like receptor subfamily B member 1 (chains G, H)
HLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTAPWITRIPQELVKKGQFP
IPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVTLQ
CDSQVAFDGFILCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSNS
PYEWSLPSDLLELLVLGVSKKPSLSVQPGPIVAPEETLTLQCGSDAGYNRFVLYKDGERD
FLQLAGAQPQAGLSQANFTLGPVSRSYGGQYRCYGAHNLSSEWSAPSDPLDILIAGQFYD
RVSLSVQPGPTVASGENVTLLCQSQGWMQTFLLTKEGAADDPWRLRSTYQSQKYQAEFPM
GPVTSAHAGTYRCYGSQSSKPYLLTHPSDPLELHHHHHH

Primary citation

Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex. Wang, Q., Song, H., Cheng, H. et al. Cell Mol Immunol (2019). DOI 10.1038/s41423-019-0258-5 · 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
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
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

About this viewer

MolViewer shows 6AEE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.