6E3K: Interferon gamma

Interferon gamma signalling complex with IFNGR1 and IFNGR2. Determined by X-ray diffraction at 3.25 Å resolution. Released 27 Feb 2019.

Method: X-ray diffraction
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,966
Mol. weight: 146.39 kDa
Ligands: CYS, NAG
Released: 27 Feb 2019

Explore 6E3K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E3K contains 44 α-helices and 85 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

Chain C: 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 D: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
β-strand	16-23	8	5
β-strand	26-32	7	5
β-strand	41-48	8	6
α-helix	56	1
β-strand	57-63	7	6
β-strand	67-69	3	5
α-helix	71-73	3
β-strand	81-89	9	6
β-strand	92-93	2	6
β-strand	97-98	2	6
α-helix	99-101	3
β-strand	102	1	6
α-helix	104-107	4
β-strand	109	1	5
α-helix	111-113	3
β-strand	114-119	6	7
β-strand	123-129	7	7
α-helix	130-131	2
β-strand	152-161	10	8
β-strand	164-171	8	8
β-strand	178	1	9
β-strand	183	1	9
β-strand	184-188	5	7
β-strand	195-204	10	8
α-helix	209	1
β-strand	210	1	8
α-helix	211-216	6
β-strand	217-220	4	8

Chain E: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	29-30	2	10
α-helix	31-33	3
β-strand	34-39	6	11
β-strand	41	1	12
β-strand	46-50	5	11
α-helix	60-61	2
β-strand	62-68	7	10
β-strand	75-76	2	10
β-strand	87-89	3	10
β-strand	93-95	3	11
β-strand	110-111	2	13
β-strand	112-119	8	10
β-strand	122-124	3	10
β-strand	127-128	2	10
α-helix	129-131	3
β-strand	132-133	2	13
α-helix	134-137	4
β-strand	139	1	12
α-helix	142-143	2
β-strand	144-151	8	14
β-strand	152	1	15
β-strand	154-160	7	14
β-strand	171-181	11	16
β-strand	187-192	6	16
β-strand	196-198	3	14
β-strand	207-218	12	16
β-strand	224-229	6	16
α-helix	230-232	3
β-strand	233-236	4	16
β-strand	238	1	15

Chain I: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	29-30	2	17
α-helix	31-33	3
β-strand	34-39	6	18
β-strand	41	1	19
β-strand	46-50	5	18
β-strand	62-68	7	17
β-strand	75-76	2	17
β-strand	87-89	3	17
β-strand	93-95	3	18
β-strand	111	1	20
β-strand	112-119	8	17
β-strand	122-124	3	17
β-strand	127-128	2	17
α-helix	129-131	3
β-strand	132	1	20
α-helix	134-137	4
β-strand	139	1	19
α-helix	142-143	2
β-strand	144-151	8	21
β-strand	154-160	7	21
β-strand	171-181	11	22
β-strand	187-192	6	22
β-strand	196-198	3	21
β-strand	207-218	12	22
β-strand	224-229	6	22
α-helix	230-232	3
β-strand	233-236	4	22

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

>6E3K_1 Interferon gamma (chains A, B)
GPGSQDPYVKEAENLKKYFNAGHSDVADNGTLFLGILKNWKEESDRKIMQSQIVSFYFKL
FKNFKDDQSIQKSVETIKEDMNVKFFNSNKKKRDDFEKLTNYSVTDLNVQRKAIHELIQV
MAELSPAAKTGKRKRSQAAAHHHHHHHH

Sequence of entity 2 (C, D), FASTA

>6E3K_2 Interferon gamma receptor 1 (chains C, D)
GSEMGTADLGPSSVPTPTNVTIESYNMNPIVYWEYQIMPQVPVFTVEVKNYGVKNSEWID
ACINISHHYCNISDHVGDPSNSLWVRVKARVGQKESAYAKSEEFAVCRDGKIGPPKLDIR
KEEKQIMIDIFHPSVFVNGDEQEVDYDPETICYIRVYNVYVRKNGSEIKYKILTQNEDDC
DEIRCQLAIPVSSLNSQYCVSAEGVLNVWGVTTEKSKEVCITIFNSSIKGSAAAHHHHHH
HH

Sequence of entity 3 (E, I), FASTA

>6E3K_3 Interferon gamma receptor 2 (chains E, I)
GSSQLPAPQHPKIRLYNAEQVLSWEPVALSNSTRPVVYQVQFKYTDSKWFTADIMSIGVN
CTQITATECDFTAASPSAGFPMDFNVTLRLRAELGALHSAWVTMPWFQHYRNVTVGPPEN
IEVTPGEGSLIIRFSSPFDIADTSTAFFCYYVHYWEKGGIQQVKGPFRSNSISLDNLKPS
RVYCLQVQAQLLWNKSNIFRVGHLSNISCYETMADASTELQQAAAHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CYS	Cysteine	C3 H7 N O2 S	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

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

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
1HIG 3.5 Å, Three-dimensional structure of recombinant human interferon-gamma.
6E3L 3.8 Å, Interferon gamma signalling complex with IFNGR1 and IFNGR2

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