PDB-7ib3: Crystal structure of Zika NS2B-NS3 protease in complex with fragm...

ID or keywords:

Entry

Database: PDB / ID: 7ib3

Title

Crystal structure of Zika NS2B-NS3 protease in complex with fragment EOS103134 from ECBL-96

Components

NS2B co-factor
NS3 protease

Keywords

VIRAL PROTEIN / crystallographic fragment screening / NS2B-NS3 Zika protease / ECBL-96 fragment library

Function / homology

Function and homology information

symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm ...
Similarity search - Function

Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology

Biological species

Zika virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.61 Å

Authors

Benz, L.S. / Wollenhaupt, J. / Jirgensons, A. / Miletic, T. / Mueller, U. / Weiss, M.S.

Funding support

Germany, 1items

Citation

Journal: Rsc Med Chem / Year: 2025
Title: From fragments to follow-ups: rapid hit expansion by making use of EU-OPENSCREEN resources.
Authors: Benz, L.S. / Wollenhaupt, J. / Jirgensons, A. / Miletic, T. / Mueller, U. / Weiss, M.S.

History

Deposition	May 21, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ib3.cif.gz	221.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7ib3.ent.gz		Display	PDB format
PDBx/mmJSON format	7ib3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ib3_validation.pdf.gz	669.7 KB	Display	wwPDB validaton report
Full document	7ib3_full_validation.pdf.gz	670.7 KB	Display
Data in XML	7ib3_validation.xml.gz	19.3 KB	Display
Data in CIF	7ib3_validation.cif.gz	25.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/7ib3 ftp://data.pdbj.org/pub/pdb/validation_reports/ib/7ib3	HTTPS FTP

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Group deposition

ID	G_1002347 (18 entries) 7iaq 7iar 7ias 7iat 7iau 7iav 7iaw 7iax 7iay 7iaz
Title	Zika NS2B-NS3 protease vs. ECBL-96
Type	changed state
Description	Zika NS2B-NS3 protease in complex with fragments from the ECBL-96 Library.

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#103 - Jul 2008 Dengue Virus similarity (41) #197 - May 2016 Zika Virus similarity (41)

Deposited unit

A: NS2B co-factor

B: NS3 protease

C: NS2B co-factor

D: NS3 protease

hetero molecules

49.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NS2B co-factor

B: NS3 protease

defined by author&software
24.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: NS2B co-factor

D: NS3 protease

hetero molecules

defined by author&software
24.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.450, 60.450, 214.730
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	NS2B co-factor Mass: 5865.384 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A142IX72
#2: Protein	NS3 protease Mass: 18877.396 Da / Num. of mol.: 2 / Mutation: C143S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A142IX72
#3: Chemical	ChemComp-A1CDR / 1-(1-ethyl-1H-pyrrol-3-yl)methanamine Mass: 124.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₂N₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate pH 4.6, 0.2 M ammonium sulfate, 24 % (w/v) PEG 2000 Time: 2-3 days

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.9184 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2024

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9184 Å / Relative weight: 1

Reflection

Resolution: 1.61→39.71 Å / Num. obs: 52753 / % possible obs: 100 % / CC_1/2: 1 / R_merge(I) obs: 0.072 / R_rim(I) all: 0.075 / Net I/σ(I): 19.77 / Num. measured all: 602472

Reflection shell

Diffraction-ID: 1 / % possible obs: 100 %

Resolution (Å)	R_merge(I) obs	Num. measured obs	Num. unique obs	CC_1/2	R_rim(I) all	Net I/σ(I) obs
1.61-1.71	1.141	98810	8341	0.746	1.193	1.92
1.71-1.83	0.625	93000	7895	0.906	0.654	3.56
1.83-1.97	0.353	79837	7332	0.97	0.371	6.19
1.97-2.16	0.205	82431	6826	0.991	0.214	11.44
2.16-2.41	0.125	73403	6191	0.996	0.131	18.98
2.41-2.79	0.09	59385	5490	0.998	0.095	25.47
2.79-3.41	0.05	53500	4715	0.999	0.053	46.15
3.41-4.81	0.032	39737	3734	1	0.033	66.16

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.61→39.71 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2014	2099	3.98 %
R_work	0.1811	-	-
obs	0.1819	52741	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.61→39.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2868	0	9	156	3033

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2953
X-RAY DIFFRACTION	f_angle_d	1.041	4003
X-RAY DIFFRACTION	f_dihedral_angle_d	6.622	416
X-RAY DIFFRACTION	f_chiral_restr	0.068	442
X-RAY DIFFRACTION	f_plane_restr	0.008	520

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.61-1.65	0.2983	137	0.2629	3309	X-RAY DIFFRACTION	100
1.65-1.69	0.2855	137	0.2516	3304	X-RAY DIFFRACTION	100
1.69-1.73	0.2734	137	0.2424	3320	X-RAY DIFFRACTION	100
1.73-1.79	0.2708	138	0.2088	3316	X-RAY DIFFRACTION	100
1.79-1.84	0.2355	137	0.1966	3303	X-RAY DIFFRACTION	100
1.84-1.91	0.2163	138	0.1828	3334	X-RAY DIFFRACTION	100
1.91-1.99	0.2209	138	0.1759	3326	X-RAY DIFFRACTION	100
1.99-2.08	0.1974	139	0.1825	3344	X-RAY DIFFRACTION	100
2.08-2.19	0.1998	139	0.1795	3358	X-RAY DIFFRACTION	100
2.19-2.32	0.19	139	0.165	3365	X-RAY DIFFRACTION	100
2.32-2.5	0.1951	140	0.1678	3377	X-RAY DIFFRACTION	100
2.5-2.75	0.2223	142	0.1901	3402	X-RAY DIFFRACTION	100
2.75-3.15	0.1865	141	0.1904	3413	X-RAY DIFFRACTION	100
3.15-3.97	0.1889	144	0.1715	3480	X-RAY DIFFRACTION	100
3.97-39.71	0.1862	153	0.1691	3691	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	6.6093	-0.8303	0.1651	1.8479	0.53	1.7394	-0.0242	-0.8476	0.159	0.1876	0.0856	0.0827	-0.0897	-0.1538	-0.0853	0.1896	-0.0251	0.0304	0.2318	0.06	0.1847	16.8571	-17.7259	24.9211
2	4.1151	0.8166	1.2094	4.3721	-0.1596	3.7986	0.5196	0.4877	-0.7071	-0.1403	-0.0461	-0.4985	0.4574	0.8015	-0.458	0.2951	0.1261	-0.0329	0.3292	-0.0441	0.2741	32.9319	-25.5057	8.5491
3	2.9477	-0.4395	-1.0227	3.3033	-0.5348	4.5636	0.0327	0.1405	-0.2658	-0.0316	-0.011	0.198	0.055	-0.4031	-0.0482	0.101	0.0043	-0.0164	0.1673	0.0087	0.1625	8.6927	-20.1769	15.2163
4	7.1654	0.2156	-2.5758	2.53	-0.5542	4.0579	0.2317	0.4231	-0.0535	0.061	-0.1315	0.3	0.0478	-0.842	-0.1336	0.2125	0.0066	-0.0465	0.3964	-0.0094	0.2366	5.1425	-19.5517	6.6766
5	3.8937	-0.5637	0.3982	1.2896	0.1524	1.6682	0.0629	-0.152	0.0912	0.0604	-0.0503	-0.0979	-0.1193	0.0235	-0.0053	0.1576	-0.003	0.0089	0.1448	0.0215	0.1528	21.9347	-17.2807	18.3967
6	5.0656	-0.9656	-0.102	5.7769	0.8374	4.7655	0.0685	-0.1265	0.2844	0.1428	0.0407	-0.1588	-0.1389	0.119	-0.0462	0.1186	-0.0287	-0.0123	0.1805	0.0281	0.1572	23.0784	-16.4801	17.5563
7	6.6312	-1.2173	-1.6923	5.4779	0.8991	5.7759	-0.0418	0.3387	0.013	-0.3965	0.1398	0.414	-0.058	-0.4607	-0.1493	0.1602	-0.025	-0.0565	0.2583	0.0515	0.1873	4.3349	-45.1553	30.772
8	2.8561	1.3654	-0.7761	4.1071	1.7697	7.4661	0.1994	-0.1021	0.1186	0.1468	-0.1603	-0.1866	-0.1882	0.5058	-0.0912	0.1845	-0.063	-0.0288	0.3162	0.0894	0.2587	26.5828	-36.8869	36.9719
9	3.6181	1.6091	-0.4255	0.9278	-0.3595	2.4461	-0.0765	0.1133	0.0091	-0.021	0.1963	0.5877	-0.0425	-0.2168	-0.0601	0.1325	0.0208	-0.0022	0.2472	0.0609	0.2785	-1.3244	-44.8399	37.2141
10	2.0474	0.5457	-0.2585	1.4342	-0.6029	3.3683	0.0259	-0.0192	-0.0286	0.0757	-0.0306	0.0694	0.0525	-0.2426	0.0047	0.1402	-0.0254	0.0145	0.1706	0.0177	0.1834	8.9902	-44.7109	40.8118
11	4.9074	2.3646	0.406	3.978	1.6831	5.8083	-0.0863	0.1763	-0.1341	-0.1442	0.1021	-0.3294	0.1218	0.3696	0.0432	0.1404	0.0205	0.0297	0.1938	0.0591	0.1796	23.046	-43.1087	29.9769
12	2.6033	0.6329	-0.1262	2.998	-0.0741	2.3325	0.0451	0.0687	-0.1225	0.1157	-0.1056	-0.0026	-0.0205	0.2048	0.0254	0.12	-0.0043	0.0031	0.1729	0.0389	0.1242	19.3119	-41.7304	35.1547

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 49 through 73 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 74 through 88 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 18 through 53 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 54 through 71 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 72 through 137 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 138 through 170 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 50 through 64 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 65 through 88 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 14 through 34 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 35 through 106 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 107 through 118 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 119 through 170 )

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