5JER: Rotavirus NSP1

Structure of Rotavirus NSP1 bound to IRF-3. Determined by X-ray diffraction at 2.91 Å resolution. Released 15 Jun 2016.

Method: X-ray diffraction
Resolution: 2.91 Å
Organisms: Rotavirus A, Homo sapiens
Chains: 8
Atoms: 7,710
Mol. weight: 116.63 kDa
Released: 15 Jun 2016

Explore 5JER in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JER contains 33 α-helices and 68 β-strands across 8 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: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	191-196	6
β-strand	198	1	5
β-strand	200	1	5
β-strand	202	1	6
β-strand	204-209	6	7
β-strand	214-220	7	7
β-strand	226-229	4	8
β-strand	241-244	4	8
α-helix	245-247	3
α-helix	258-265	8
β-strand	272-277	6	8
β-strand	280-285	6	8
β-strand	289	1	1
β-strand	291-296	6	7
β-strand	309-310	2	7
β-strand	317-321	5	8
α-helix	322-333	12
α-helix	339-341	3
β-strand	343-348	6	7
α-helix	358-360	3
β-strand	363-369	7	7
α-helix	370-381	12
β-strand	388-391	4	9
β-strand	395	1	6
β-strand	401-404	4	9
α-helix	405-416	12

Chains B, D, F and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	488	1	1

Chain C: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	193-195	3
β-strand	202	1	10
β-strand	204-209	6	11
β-strand	214-220	7	11
β-strand	226-229	4	12
β-strand	241-244	4	12
α-helix	245-249	5
α-helix	255-266	12
β-strand	272-276	5	12
β-strand	280-285	6	12
β-strand	289	1	2
β-strand	291-296	6	11
β-strand	309-311	3	11
β-strand	317-321	5	12
α-helix	322-333	12
α-helix	338-341	4
β-strand	343-348	6	11
α-helix	358-360	3
β-strand	363-369	7	11
α-helix	370-382	13
β-strand	389-391	3	13
β-strand	395	1	10
β-strand	401-403	3	13
α-helix	405-416	12

Chain E: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	191-195	5
α-helix	200-203	4
β-strand	204-210	7	14
β-strand	214-220	7	14
β-strand	226-229	4	15
β-strand	241-244	4	15
α-helix	245-249	5
α-helix	255-265	11
β-strand	272-277	6	15
β-strand	280-285	6	15
β-strand	289	1	3
β-strand	291-296	6	14
β-strand	309-310	2	14
α-helix	311-312	2
β-strand	317-321	5	15
α-helix	322-334	13
α-helix	338-341	4
β-strand	343-348	6	14
α-helix	358-360	3
β-strand	363-369	7	14
α-helix	370-383	14
β-strand	388-391	4	16
β-strand	401-404	4	16
α-helix	405-417	13

Chain G: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	191-196	6
β-strand	202	1	17
β-strand	204-210	7	18
β-strand	213-220	8	18
β-strand	226-229	4	19
β-strand	241-244	4	19
α-helix	245-249	5
α-helix	255-266	12
β-strand	272-277	6	19
β-strand	280-285	6	19
β-strand	289	1	4
β-strand	291-296	6	18
β-strand	309-310	2	18
β-strand	317-321	5	19
α-helix	322-333	12
α-helix	339-341	3
β-strand	343-348	6	18
β-strand	363-369	7	18
α-helix	370-382	13
β-strand	389-391	3	20
β-strand	395	1	17
β-strand	401-403	3	20
α-helix	405-416	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rotavirus NSP1 peptide	B, D, F, H	protein	19	Rotavirus A	Q99FX5
Interferon regulatory factor 3	A, C, E, G	protein	242	Homo sapiens	Q14653 (AlphaFold model)

Sequence of entity 1 (B, D, F, H), FASTA

>5JER_1 Rotavirus NSP1 peptide (chains B, D, F, H)
STLTEEFELLISNSEDDWE

Sequence of entity 2 (A, C, E, G), FASTA

>5JER_2 Interferon regulatory factor 3 (chains A, C, E, G)
SEFENPLKRLLVPGEEWEFEVTAFYRGRQVFQQTISCPEGLRLVGSEVGDRTLPGWPVTL
PDPGMSLTDRGVMSYVRHVLSCLGGGLALWRAGQWLWAQRLGHCHTYWAVSEELLPNSGH
GPDGEVPKDKEGGVFDLGPFIVDLITFTEGSGRSPRYALWFCVGESWPQDQPWTKRLVMV
KVVPTCLRALVEMARVGGASSLENTVDLHISNSHPLSLTSDQYKAYLQDLVEGMDFQGPG
ES

Primary citation

Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins. Zhao, B., Shu, C., Gao, X. et al. Proc Natl Acad Sci U S A (2016) 113:E3403-E3412. DOI 10.1073/pnas.1603269113 · PubMed

Other PDB entries of the same protein (UniProt Q99FX5), best resolution first:

5JEO 1.72 Å, Phosphorylated Rotavirus NSP1 in complex with IRF-3

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