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

ID or keywords:

Entry

Database: PDB / ID: 7iay

Title

Crystal structure of Zika NS2B-NS3 protease in complex with fragment EOS103107 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: 1.57 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	7iay.cif.gz	159.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7iay.ent.gz		Display	PDB format
PDBx/mmJSON format	7iay.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7iay_validation.pdf.gz	689.7 KB	Display	wwPDB validaton report
Full document	7iay_full_validation.pdf.gz	694.7 KB	Display
Data in XML	7iay_validation.xml.gz	19 KB	Display
Data in CIF	7iay_validation.cif.gz	25 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ia/7iay ftp://data.pdbj.org/pub/pdb/validation_reports/ia/7iay	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)	60.510, 60.510, 215.670
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-A1EHQ / 2-phenoxyethanamine Mass: 137.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₁NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / 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: 2 Å³/Da / Density % sol: 38.49 %
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: 1.57→46.29 Å / Num. obs: 57290 / % possible obs: 100 % / CC_1/2: 0.996 / R_merge(I) obs: 0.169 / R_rim(I) all: 0.178 / Net I/σ(I): 9.12 / Num. measured all: 630865

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	% possible obs (%)	R_merge(I) obs	Num. measured obs	Num. unique obs	CC_1/2	R_rim(I) all	Net I/σ(I) obs
1.57-1.66		100	1.245	98905	9076	0.361	1.306	1.37
1.66-1.78		100	0.768	96460	8599	0.643	0.805	2.22
1.78-1.92		100	0.475	86886	7938	0.829	0.499	3.69
1.92-2.1		99.9	0.307	84093	7396	0.923	0.322	6.57
2.1-2.35		100	0.224	79556	6724	0.963	0.234	10.87
2.35-2.71		100	0.18	65706	5970	0.973	0.189	13.67
2.71-3.32		100	0.128	54479	5118	0.987	0.135	20.06
3.32-4.69		100	0.107	41802	4054	0.994	0.113	24.27
	4.69	99.8	0.093	22978	2415	0.994	0.098	23.66

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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: 1.57→46.29 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2991	2100	3.67 %
R_work	0.271	-	-
obs	0.2721	57288	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.57→46.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2881	0	10	122	3013

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2944
X-RAY DIFFRACTION	f_angle_d	0.605	3984
X-RAY DIFFRACTION	f_dihedral_angle_d	12.159	1064
X-RAY DIFFRACTION	f_chiral_restr	0.049	439
X-RAY DIFFRACTION	f_plane_restr	0.005	516

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 (%)
1.57-1.61	0.387	137	0.336	3599	X-RAY DIFFRACTION	100
1.61-1.65	0.3361	138	0.3252	3629	X-RAY DIFFRACTION	100
1.65-1.69	0.3279	137	0.3132	3596	X-RAY DIFFRACTION	100
1.69-1.74	0.3774	138	0.3051	3609	X-RAY DIFFRACTION	100
1.74-1.8	0.3428	137	0.2952	3616	X-RAY DIFFRACTION	100
1.8-1.86	0.3037	139	0.2783	3648	X-RAY DIFFRACTION	100
1.86-1.94	0.3203	138	0.2672	3623	X-RAY DIFFRACTION	100
1.94-2.02	0.312	139	0.2729	3645	X-RAY DIFFRACTION	100
2.02-2.13	0.2989	138	0.2742	3632	X-RAY DIFFRACTION	100
2.13-2.26	0.3131	139	0.2589	3663	X-RAY DIFFRACTION	100
2.26-2.44	0.3035	141	0.2619	3690	X-RAY DIFFRACTION	100
2.44-2.68	0.3114	140	0.2816	3692	X-RAY DIFFRACTION	100
2.68-3.07	0.2899	143	0.2714	3743	X-RAY DIFFRACTION	100
3.07-3.87	0.272	144	0.2618	3790	X-RAY DIFFRACTION	100
3.87-46.29	0.2763	152	0.2557	4013	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	0.0873	-0.1929	0.1539	0.7822	-0.7506	0.7521	0.0458	-0.1714	-0.1495	0.2499	0.1189	-0.0175	-0.1125	-0.1328	0.3	0.028	-0.0216	-0.0185	0.2338	0.0571	0.3116	3.697	-21.9792	18.1259
2	0.4294	-0.0385	0.1458	0.3118	-0.4097	0.5581	-0.3662	-0.1147	-0.1422	0.0204	-0.115	-0.0093	0.2296	-0.0497	-0.293	0.0792	-0.0269	0.0563	0.401	0.071	0.437	16.5655	-9.4922	29.6495
3	0.8689	-0.2933	-0.0822	0.538	-0.0093	0.1687	0.0552	-0.2173	-0.0889	0.2619	0.101	0.1646	-0.0293	-0.241	0.1711	0.4121	0.0228	0.0329	0.2494	0.0996	0.1742	22.7099	-17.2036	34.6652
4	0.2133	-0.0942	0.016	0.2202	-0.1941	0.1927	0.0272	-0.0555	0.0113	0.0944	-0.2662	-0.0709	0.0029	-0.0159	-0.0083	0.205	-0.0384	-0.0493	0.1833	-0.0246	0.2115	32.5789	-23.0477	12.9057
5	2.8029	-1.937	-1.3703	1.3467	1.0151	1.0501	-0.1399	0.1319	-0.0796	-0.1096	-0.1867	0.0969	-0.0366	-0.196	-0.4578	0.1609	0.0944	-0.0835	0.1111	-0.0528	0.3195	36.3335	-27.0146	10.8695
6	0.3861	-0.2161	-0.0284	0.1095	0.0034	0.0335	-0.0441	0.2088	-0.0954	0.091	0.1427	0.294	0.083	-0.1642	0.0045	0.118	-0.0088	0.0072	0.1626	0.0581	0.2043	6.7094	-21.1821	18.0152
7	0.9848	0.744	0.6039	0.5704	0.4789	0.465	-0.0274	0.2246	0.0103	-0.1191	0.2237	0.0507	-0.0733	0.0212	0.3443	0.1422	0.0422	0.0364	0.1327	0.0793	0.0959	12.431	-18.7191	10.6745
8	0.1894	-0.0956	-0.2276	0.4866	0.0118	0.2725	-0.0056	-0.0191	0.0639	-0.124	-0.0298	0.4513	0.0957	-0.7139	-0.0182	0.1742	0.0166	-0.0492	0.3426	0.0183	0.2052	5.1988	-19.6705	6.7671
9	0.3385	-0.0484	-0.1884	0.3192	-0.1598	0.8558	-0.1528	0.0625	0.2811	0.1039	0.1321	-0.0545	-0.3053	0.1161	0.2795	0.1911	-0.0199	-0.0446	0.1517	0.0564	0.2266	20.0513	-12.8747	12.1849
10	0.3624	-0.4893	0.2269	0.669	-0.3113	0.138	-0.1193	-0.3224	-0.0783	0.12	0.0965	0.0553	-0.1153	0.0411	-0.0096	0.1555	-0.0117	-0.0197	0.2144	0.0232	0.1121	21.8818	-18.7829	25.0034
11	0.5414	-0.1697	0.2167	0.0974	-0.0831	0.0763	0.0811	0.0344	0.0299	0.0173	-0.1001	-0.0156	-0.044	0.0541	0.0011	0.1245	-0.0111	-0.0111	0.117	0.0591	0.1744	23.5315	-18.1963	18.7998
12	0.1352	0.0255	0.0024	0.4409	-0.3338	0.2489	0.0549	-0.0741	-0.2374	0.1657	-0.1628	-0.1731	0.1839	0.0041	-0.2172	0.204	0.0024	-0.072	0.1525	0.0443	0.1734	25.2146	-19.2295	15.14
13	1.2915	-0.4145	-0.3463	0.7082	-0.0764	0.155	0.1614	0.1208	0.374	-0.1603	0.0404	-0.239	-0.0878	-0.1997	0.3988	0.1496	0.1938	0.0101	0.3796	0.032	0.1661	-1.9139	-37.1822	40.8717
14	0.0517	-0.0049	0.0127	0.0216	0.0059	0.0057	-0.0398	-0.0582	-0.0677	0.2047	0.1831	-0.2339	-0.2233	-0.0479	0.0004	0.2019	0.0495	0.0047	0.1416	0.0239	0.1576	2.3061	-47.847	30.4805
15	0.4912	-0.1367	-0.0884	0.9357	-0.2859	0.1257	-0.0237	0.4846	0.1449	-0.1953	-0.1203	-0.1288	0.0799	0.0165	-0.1297	0.1961	0.0321	-0.0101	0.6074	-0.051	0.1275	15.1844	-47.407	20.7431
16	0.1802	0.1666	0.2162	0.5527	-0.4499	2.872	-0.1198	-0.2388	0.1936	0.337	-0.4738	0.0603	-0.0597	0.0713	-1.1437	0.1909	-0.0874	0.0364	0.3057	-0.0282	0.2532	27.8262	-36.9981	40.5971
17	1.1482	0.9554	0.135	1.1588	0.2494	0.2987	-0.0536	0.0794	0.0078	-0.0524	0.0263	0.0593	0.0218	-0.0074	0.1813	0.2892	-0.1759	0.0682	0.2277	-0.1112	0.149	30.6138	-32.2843	41.523
18	0.5111	-0.1998	0.1233	0.1876	-0.2038	0.3826	0.0637	-0.0286	-0.1426	0.0495	0.2269	0.3782	0.1469	-0.3469	0.9739	0.1507	0.0046	-0.0254	0.2151	0.2487	0.2157	-1.1164	-44.7842	37.3453
19	0.1614	0.132	-0.1375	0.1132	-0.1171	0.111	0.0216	-0.1743	0.0091	0.063	0.0671	-0.0299	-0.1381	-0.144	-0.0001	0.1644	0.0089	0.0167	0.1396	0.0192	0.1437	7.3232	-43.2999	41.5598
20	0.0114	0.0071	0.0043	0.0429	-0.0453	0.0471	0.0752	0.0753	0.0437	-0.3238	-0.1403	0.0025	-0.2526	-0.4123	-0.0001	0.2443	0.046	0.0466	0.4804	-0.0722	0.2221	-2.1249	-40.4664	46.3492
21	0.5518	-0.2078	0.0949	0.2814	-0.1567	0.6038	-0.0248	-0.2815	-0.0989	-0.1203	0.0989	-0.0577	0.046	0.201	0.1073	0.1319	0.0017	0.0245	0.1503	0.0422	0.1466	12.8013	-47.9392	44.0534
22	1.9362	-0.3397	-0.1326	0.5262	0.0779	0.0226	-0.094	0.3223	0.5319	-0.1188	0.1142	-0.0815	-0.0825	-0.0298	-0.069	0.1038	0.0078	0.0229	0.1737	0.0311	0.1196	9.2026	-40.5502	27.2277
23	0.3931	0.3426	0.1779	0.4821	-0.0158	0.2205	0.0677	0.2731	-0.0169	-0.0599	0.0405	-0.1243	0.0001	0.0659	0.0237	0.1398	-0.0047	0.0206	0.2393	0.0138	0.1084	23.1502	-43.1811	30.1063
24	0.2478	-0.1081	0.0058	0.1629	0.1117	0.0839	0.0319	0.1593	0.0417	-0.1669	-0.0346	-0.1219	-0.1308	0.0197	0.0011	0.1089	-0.0003	0.0127	0.1128	0.0376	0.1335	18.6374	-42.6966	34.6747
25	0.4066	0.069	0.2866	0.9541	-0.3633	0.4395	-0.078	0.2301	-0.0638	-0.1816	-0.097	-0.2824	0.2062	0.1851	-0.1691	0.1664	0.0178	0.0559	0.115	0.0419	0.1073	21.0245	-41.039	37.829

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 49 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 68 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 69 through 83 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 84 through 88 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 18 through 42 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 43 through 53 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 54 through 71 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 72 through 94 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 95 through 118 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 119 through 155 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 156 through 170 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 50 through 54 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 55 through 59 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 60 through 69 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 70 through 83 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 84 through 88 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 14 through 34 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 35 through 53 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 54 through 62 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 63 through 94 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 95 through 106 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 107 through 118 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 119 through 155 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 156 through 171 )

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

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