6E3L: Interferon gamma

Interferon gamma signalling complex with IFNGR1 and IFNGR2. Determined by X-ray diffraction at 3.8 Å resolution. Released 27 Feb 2019.

Method: X-ray diffraction
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,976
Mol. weight: 147.24 kDa
Ligands: NAG, CYS
Released: 27 Feb 2019

Explore 6E3L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E3L contains 44 α-helices and 81 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	3-14	12
α-helix	20-23	4
α-helix	30-33	4
α-helix	39-59	21
α-helix	67-80	14
α-helix	86-97	12
α-helix	103-118	16

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	3-14	12
α-helix	20-23	4
α-helix	30-33	4
α-helix	39-59	21
α-helix	67-80	14
α-helix	86-97	12
α-helix	103-118	16
α-helix	122-123	2

Chains C and D: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
β-strand	16-23	8	1
β-strand	26-32	7	1
β-strand	41-48	8	2
α-helix	56	1
β-strand	57-63	7	2
β-strand	67-69	3	1
α-helix	71-73	3
β-strand	81-89	9	2
β-strand	92-93	2	2
β-strand	97-98	2	2
α-helix	99-101	3
β-strand	102	1	2
α-helix	104-107	4
β-strand	109	1	1
α-helix	111-113	3
β-strand	114-119	6	3
β-strand	123-129	7	3
α-helix	130-131	2
β-strand	152-161	10	4
β-strand	164-171	8	4
β-strand	178	1	3
β-strand	182-188	7	3
β-strand	195-204	10	4
α-helix	209	1
β-strand	210	1	4
α-helix	211-216	6
β-strand	217-220	4	4

Chain E: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
β-strand	34-39	6	9
β-strand	41	1	10
β-strand	46-50	5	9
α-helix	60-61	2
β-strand	62-68	7	11
β-strand	75-76	2	11
β-strand	87-89	3	11
β-strand	93-95	3	9
β-strand	110-111	2	12
β-strand	112-119	8	11
β-strand	122-123	2	11
β-strand	127-128	2	11
α-helix	129-131	3
β-strand	132-133	2	12
α-helix	134-137	4
β-strand	139	1	10
α-helix	142-143	2
β-strand	144-151	8	13
β-strand	154-160	7	13
β-strand	171-181	11	14
β-strand	187-192	6	14
β-strand	196-198	3	13
β-strand	207-218	12	14
β-strand	224-229	6	14
α-helix	230-232	3
β-strand	233-236	4	14

Chain I: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	29-30	2	15
α-helix	31-33	3
β-strand	34-39	6	16
β-strand	41	1	17
β-strand	46-50	5	16
β-strand	62-68	7	15
β-strand	75-76	2	15
β-strand	87-89	3	15
β-strand	93-95	3	16
β-strand	111	1	18
β-strand	112-119	8	15
β-strand	122-124	3	15
β-strand	127-128	2	15
α-helix	129-131	3
β-strand	132	1	18
α-helix	134-137	4
β-strand	139	1	17
α-helix	142-143	2
β-strand	144-151	8	19
β-strand	154-160	7	19
β-strand	171-181	11	20
β-strand	187-192	6	20
β-strand	196-198	3	19
β-strand	207-218	12	20
β-strand	224-229	6	20
α-helix	230-232	3
β-strand	233-236	4	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interferon gamma	A, B	protein	148	Homo sapiens	P01579 (AlphaFold model)
Interferon gamma receptor 1	C, D	protein	242	Homo sapiens	P15260 (AlphaFold model)
Interferon gamma receptor 2	E, I	protein	233	Homo sapiens	P38484 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6E3L_1 Interferon gamma (chains A, B)
GPGSQDPYVKEAENLKKYFNAGHSDVADNGTLFLGILKNWKEESDRKIMQSQIVSFYFKL
FKNFKDDQSIQKSVETIKEDMNVKFFNSNKKKRDDFEKLTNYSVTDLNVQRKAIHELIQV
MAELSPAAKTGKRKRSQAAAHHHHHHHH

Sequence of entity 2 (C, D), FASTA

>6E3L_2 Interferon gamma receptor 1 (chains C, D)
GSEMGTADLGPSSVPTPTNVTIESYNMNPIVYWEYQIMPQVPVFTVEVKNYGVKNSEWID
ACINISHHYCNISDHVGDPSNSLWVRVKARVGQKESAYAKSEEFAVCRDGKIGPPKLDIR
KEEKQIMIDIFHPSVFVNGDEQEVDYDPETICYIRVYNVYVRKNGSEIKYKILTQNEDDC
DEIRCQLAIPVSSLNSQYCVSAEGVLNVWGVTTEKSKEVCITIFNSSIKGSAAAHHHHHH
HH

Sequence of entity 3 (E, I), FASTA

>6E3L_3 Interferon gamma receptor 2 (chains E, I)
GSSQLPAPQHPKIRLYNAEQVLSWEPVALSNSTRPVVYQVQFKYTDSKWFTADIMSIGVN
CTQITATECDFTAASPSAGFPMDFNVTLRLRAELGALHSAWVTMPWFQHYRNVTVGPPEN
IEVTPGEGSLIIRFSSPFDIADTSTAFFCYYVHYWEKGGIQQVKGPFRSNSISLDNLKPS
RVYCLQVQAQLLWNKSNIFRVGHLSNISCYETMADASTELQQAAAHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
CYS	Cysteine	C3 H7 N O2 S	2

Primary citation

Structure of the IFN gamma receptor complex guides design of biased agonists. Mendoza, J.L., Escalante, N.K., Jude, K.M. et al. Nature (2019) 567:56-60. DOI 10.1038/s41586-019-0988-7 · PubMed

Other PDB entries of the same protein (UniProt P01579 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FYH 2.04 Å, 1:1 complex between an interferon gamma single-chain variant and its receptor
3BES 2.2 Å, Structure of a Poxvirus ifngbp/ifng Complex
1EKU 2.9 Å, Crystal structure of a biologically active single chain mutant of human ifn-gamma
1FG9 2.9 Å, 3:1 complex of interferon-gamma receptor with interferon-gamma dimer
9VNP 3.02 Å, The complexes of IFN-gamma and A01BM-03 Fab
6E3K 3.25 Å, Interferon gamma signalling complex with IFNGR1 and IFNGR2
1HIG 3.5 Å, Three-dimensional structure of recombinant human interferon-gamma.

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