6K60: PDB entry 6K60

Structural and functional basis for HLA-G isoform recognition of immune checkpoint receptor LILRBs. Determined by X-ray diffraction at 3.15 Å resolution. Released 27 Nov 2019.

Method: X-ray diffraction
Resolution: 3.15 Å
Organism: Homo sapiens
Chains: 8
Atoms: 7,982
Mol. weight: 135.37 kDa
Released: 27 Nov 2019

Explore 6K60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K60 contains 33 α-helices and 95 β-strands across 6 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, 18 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	50-52	3
α-helix	57-84	28
β-strand	94-102	9	1
β-strand	111-118	8	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-216	3	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	254-256	3
β-strand	259-262	4	4
β-strand	270-272	3	4

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
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	36-41	6	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	78-83	6	8
β-strand	87	1	9
β-strand	91-94	4	8

Chain D: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	10
β-strand	15-17	3	11
β-strand	22-25	4	10
β-strand	36-39	4	12
α-helix	45-48	4
α-helix	52-56	5
β-strand	59-62	4	10
α-helix	67-69	3
β-strand	71-72	2	13
β-strand	73-76	4	12
α-helix	86-89	4
β-strand	92-93	2	13
β-strand	94-96	3	11
β-strand	99	1	9
β-strand	103	1	14
α-helix	119-121	3
β-strand	123	1	14
β-strand	126	1	5
β-strand	131-135	5	15
β-strand	143-146	4	15
β-strand	173-176	4	15
β-strand	177-178	2	16
β-strand	181-185	5	16
α-helix	187-190	4

Chain E: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	17
α-helix	20	1
β-strand	21-28	8	17
β-strand	31-37	7	17
β-strand	46-47	2	17
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	17
β-strand	109-118	10	17
β-strand	121-126	6	17
β-strand	133-135	3	17
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	18
α-helix	184-185	2
β-strand	186-195	10	19
β-strand	198-208	11	19
β-strand	209	1	18
β-strand	213-219	7	20
β-strand	223-224	2	20
β-strand	228-230	3	19
α-helix	231-233	3
β-strand	234-235	2	19
β-strand	241-250	10	19
α-helix	254-256	3
β-strand	257-263	7	20
β-strand	270-273	4	20

Chain F: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	21
β-strand	3	1	22
α-helix	4-5	2
β-strand	6-11	6	23
β-strand	21-30	10	23
β-strand	31	1	22
β-strand	35-41	7	24
β-strand	44-45	2	24
α-helix	46	1
β-strand	50-51	2	23
β-strand	55-56	2	23
β-strand	62-70	9	23
β-strand	78-84	7	24
β-strand	87	1	25
β-strand	91-94	4	24

Chain H: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	26
β-strand	16-17	2	25
β-strand	22-23	2	27
β-strand	24	1	26
β-strand	38-39	2	28
α-helix	45-48	4
β-strand	61-62	2	27
α-helix	67-69	3
β-strand	71	1	29
β-strand	73-74	2	28
β-strand	93	1	29
β-strand	95-99	5	25
β-strand	126	1	21
β-strand	130	1	30
β-strand	177	1	30
β-strand	184-186	3	25
α-helix	187-189	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain G	A, E	protein	277	Homo sapiens	P17693 (AlphaFold model)
Beta-2-microglobulin	B, F	protein	100	Homo sapiens	P61769 (AlphaFold model)
Peptide from Histone H2A.J	C, G	protein	9	Homo sapiens	Q9BTM1 (AlphaFold model)
Leukocyte immunoglobulin-like receptor subfamily B member 1	D, H	protein	198	Homo sapiens	Q8NHL6 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>6K60_1 HLA class I histocompatibility antigen, alpha chain G (chains A, E)
MGSHSMRYFSAAVSRPGRGEPRFIAMGYVDDTQFVRFDSDSASPRMEPRAPWVEQEGPEY
WEEETRNTKAHAQTDRMNLQTLRGYYNQSEASSHTLQWMIGCDLGSDGRLLRGYEQYAYD
GKDYLALNEDLRSWTAADTAAQISKRKCEAANVAEQRRAYLEGTCVEWLHRYLENGKEML
QRADPPKTHVTHHPVFDYEATLRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLMLRWKQ

Sequence of entity 2 (B, F), FASTA

>6K60_2 Beta-2-microglobulin (chains B, F)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, G), FASTA

>6K60_3 Peptide from Histone H2A.J (chains C, G)
RIIPRHLQL

Sequence of entity 4 (D, H), FASTA

>6K60_4 Leukocyte immunoglobulin-like receptor subfamily B member 1 (chains D, H)
MGHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTAPWITRIPQELVKKGQ
FPIPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVT
LQCDSQVAFDGFILCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDS
NSPYEWSLPSDLLELLVL

Primary citation

Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms. Kuroki, K., Matsubara, H., Kanda, R. et al. J Immunol (2019) 203:3386-3394. DOI 10.4049/jimmunol.1900562 · 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
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

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