PDB-9zrb: Crystal structure of macrodomain from Chikungunya virus in comple...

ID or keywords:

Entry

Database: PDB / ID: 9zrb

Title

Crystal structure of macrodomain from Chikungunya virus in complex with Adenosine diphosphate ribose

Components

Polyprotein P1234

Keywords

VIRAL PROTEIN / MACRO DOMAIN / alpha virus / Adenosine diphosphate ribose

Function / homology

Function and homology information

host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity ...
Similarity search - Function

Biological species

Chikungunya virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.79 Å

Authors

Chang, C. / Endre, M. / Stols, L. / Kim, Y. / Joachimiak, A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of macrodomain from Chikungunya virus
Authors: Chang, C. / Endre, M. / Stols, L. / Kim, Y. / Joachimiak, A.

History

Deposition	Dec 19, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 12, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9zrb.cif.gz	291.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9zrb.ent.gz	236.3 KB	Display	PDB format
PDBx/mmJSON format	9zrb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zr/9zrb ftp://data.pdbj.org/pub/pdb/validation_reports/zr/9zrb	HTTPS FTP

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Related structure data

Related structure data	9zraC 9zrcC C: citing same article (ref.)
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	#213 - Sep 2017 Sirtuins similarity (2) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Polyprotein P1234

B: Polyprotein P1234

C: Polyprotein P1234

D: Polyprotein P1234

hetero molecules

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

1

A: Polyprotein P1234

hetero molecules

defined by author
18.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Polyprotein P1234

hetero molecules

defined by author
19 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Polyprotein P1234

hetero molecules

defined by author
18.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Polyprotein P1234

hetero molecules

defined by author
18.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.535, 87.535, 82.530
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Polyprotein P1234 / Non-structural polyprotein Mass: 17545.863 Da / Num. of mol.: 4 / Fragment: Macrodomain, residues 1314-1473 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7S9AU77

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Non-polymers , 5 types, 491 molecules

#2: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O
#3: Chemical	ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₅O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₅O₁₄P₂
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.6 Å³/Da / Density % sol: 52.71 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: Sodium citrate PEG 4000 Isopropanol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 17-ID-2 / Wavelength: 0.97934 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2024

Radiation

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

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 1.79→50 Å / Num. obs: 65754 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.083 / R_pim(I) all: 0.035 / R_rim(I) all: 0.091 / Χ²: 0.94 / Net I/σ(I): 8.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.8-1.83	5.2	0.71	3276	0.619	0.875	0.331	0.787	0.706	98.7
1.83-1.86	5.5	0.636	3231	0.667	0.894	0.292	0.704	0.747	99.7
1.86-1.9	6.3	0.597	3325	0.789	0.939	0.257	0.652	0.779	100
1.9-1.94	6.6	0.531	3283	0.848	0.958	0.223	0.577	0.796	100
1.94-1.98	6.8	0.488	3332	0.862	0.962	0.203	0.53	0.829	100
1.98-2.03	6.9	0.404	3259	0.911	0.976	0.167	0.437	0.857	100
2.03-2.08	6.9	0.324	3344	0.941	0.985	0.133	0.351	0.888	100
2.08-2.13	6.9	0.267	3276	0.957	0.989	0.11	0.289	0.925	100
2.13-2.2	6.9	0.226	3347	0.971	0.993	0.093	0.244	0.965	100
2.2-2.27	6.8	0.198	3275	0.974	0.993	0.082	0.215	0.978	100
2.27-2.35	6.6	0.168	3321	0.98	0.995	0.071	0.183	0.962	99.8
2.35-2.44	6.3	0.147	3318	0.981	0.995	0.063	0.161	1.001	99.8
2.44-2.55	6.9	0.131	3261	0.988	0.997	0.054	0.141	1.008	99.7
2.55-2.69	6.5	0.109	3299	0.99	0.997	0.046	0.119	1.013	99.6
2.69-2.86	7.2	0.092	3307	0.993	0.998	0.037	0.099	1.053	99.8
2.86-3.08	7.2	0.077	3277	0.995	0.999	0.031	0.083	1.097	99.7
3.08-3.39	7	0.065	3292	0.996	0.999	0.027	0.071	1.123	99.3
3.39-3.88	6.6	0.057	3269	0.996	0.999	0.024	0.062	1.129	98.4
3.88-4.88	6.2	0.052	3193	0.996	0.999	0.022	0.057	1.018	96.7
4.88-50	6.8	0.048	3269	0.997	0.999	0.019	0.052	0.804	98.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-3000		data scaling
PDB_EXTRACT		data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.79→38.67 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1924	3089	4.96 %
R_work	0.1517	-	-
obs	0.1537	62303	94.13 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.79→38.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4911	0	182	475	5568

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5511
X-RAY DIFFRACTION	f_angle_d	0.799	7534
X-RAY DIFFRACTION	f_dihedral_angle_d	13.741	2190
X-RAY DIFFRACTION	f_chiral_restr	0.054	857
X-RAY DIFFRACTION	f_plane_restr	0.007	944

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 (%)
1.79-1.82	0.1811	57	0.2207	1814	X-RAY DIFFRACTION	61
1.82-1.85	0.2315	74	0.2029	1941	X-RAY DIFFRACTION	68
1.85-1.88	0.2641	109	0.1938	2306	X-RAY DIFFRACTION	81
1.88-1.92	0.2294	123	0.1932	2517	X-RAY DIFFRACTION	87
1.92-1.95	0.2496	157	0.2028	2514	X-RAY DIFFRACTION	91
1.96-1.99	0.2536	115	0.1846	2780	X-RAY DIFFRACTION	95
2-2.04	0.2412	150	0.1633	2837	X-RAY DIFFRACTION	98
2.04-2.09	0.2038	128	0.1647	2863	X-RAY DIFFRACTION	100
2.09-2.14	0.2039	150	0.1619	2866	X-RAY DIFFRACTION	100
2.14-2.2	0.2067	146	0.1515	2844	X-RAY DIFFRACTION	100
2.2-2.26	0.2006	186	0.1503	2780	X-RAY DIFFRACTION	100
2.26-2.33	0.2083	141	0.1701	2916	X-RAY DIFFRACTION	100
2.33-2.42	0.1953	150	0.1634	2840	X-RAY DIFFRACTION	100
2.42-2.51	0.2098	157	0.1625	2840	X-RAY DIFFRACTION	100
2.51-2.63	0.2065	191	0.1599	2801	X-RAY DIFFRACTION	100
2.63-2.77	0.2333	163	0.1714	2849	X-RAY DIFFRACTION	100
2.77-2.94	0.1875	176	0.15	2806	X-RAY DIFFRACTION	100
2.94-3.17	0.2058	155	0.15	2873	X-RAY DIFFRACTION	100
3.17-3.48	0.1613	134	0.1337	2810	X-RAY DIFFRACTION	99
3.49-3.99	0.1667	117	0.1248	2865	X-RAY DIFFRACTION	98
3.99-5.02	0.1329	151	0.1192	2745	X-RAY DIFFRACTION	97
5.03-38.67	0.1798	159	0.1441	2807	X-RAY DIFFRACTION	99

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	2.7307	-0.6241	2.9929	3.232	-2.3049	4.6843	0.2381	-0.043	-0.2841	-0.1351	-0.0271	0.0763	0.5302	-0.061	-0.1863	0.1731	-0.0059	0.0018	0.1162	0.0063	0.1449	-0.1364	-19.561	-4.0106
2	1.3091	0.3461	0.1887	2.7032	1.3761	2.017	0.0424	-0.1389	-0.0303	0.0564	-0.0749	-0.0088	0.0658	-0.0604	0.0079	0.0708	0.0019	0.0035	0.1188	0.0011	0.0752	8.5375	-10.3559	3.2368
3	2.3258	-3.349	-1.3332	5.6335	1.1762	4.046	-0.0985	-0.547	-0.2769	0.4798	0.1207	0.0198	0.496	0.2035	0.079	0.1547	0.0011	-0.0141	0.1865	0.0353	0.116	11.1402	-15.3554	7.5631
4	1.3487	-1.041	-0.2998	3.877	1.5045	1.4173	0.0741	-0.0262	-0.0296	-0.0563	0.0011	-0.1605	-0.0793	0.2186	-0.0865	0.0866	-0.0123	0.005	0.1398	0.0044	0.0859	13.4234	-6.7586	0.4427
5	3.0644	-0.8897	-2.4618	1.61	1.6317	6.3417	0.1215	-0.0414	0.2608	-0.0912	-0.1046	0.0281	-0.4012	-0.1326	-0.1138	0.1123	-0.0129	-0.0204	0.0883	-0.0152	0.1136	-1.2721	0.4207	2.1914
6	2.0505	0.7048	-0.0426	2.0967	-0.9858	3.1848	-0.1565	0.1262	-0.1442	-0.1971	-0.0812	-0.0585	0.2733	-0.1501	0.0016	0.1163	0.0067	-0.0107	0.0863	0.0039	0.0793	4.059	-12.4079	-7.315
7	2.0112	1.4083	0.5975	2.5638	-0.3636	2.6887	0.1642	-0.3991	0.0095	0.3864	-0.1875	0.1704	0.2078	-0.2949	0.0443	0.1405	-0.0594	0.0487	0.2131	-0.0249	0.1111	-5.2457	-7.8441	9.8959
8	2.9764	0.0424	-0.7567	2.2472	0.3908	1.6476	0.0219	-0.0844	-0.0041	-0.0768	-0.0779	0.216	0.0654	-0.1441	0.0687	0.0801	-0.0313	-0.022	0.1223	-0.0183	0.0952	-4.4736	-10.7608	-3.8571
9	4.8632	-1.1053	2.8996	4.6616	-2.358	6.7327	0.1433	0.0451	-0.225	-0.3225	0.1377	0.6544	0.418	-0.4574	-0.1877	0.129	-0.0945	0.0029	0.2331	-0.0207	0.2375	-12.4965	-17.8064	-2.469
10	1.0165	0.0325	-0.2133	5.5621	1.4859	4.1548	0.0996	0.3733	0.0767	-0.7229	-0.0425	-0.3963	-0.3317	-0.049	-0.0813	0.1732	0.0299	0.0776	0.2453	0.0601	0.1721	36.328	-17.8432	-23.8462
11	5.2738	1.0693	-1.0355	3.0318	0.8482	2.049	-0.1015	0.2078	-0.3143	-0.1775	-0.0882	0.0396	0.2847	-0.0872	0.1643	0.2115	0.0336	0.0369	0.1237	-0.0109	0.1226	32.4962	-31.6297	-19.2031
12	2.8518	-0.5044	-1.4198	0.6374	0.2417	1.8617	-0.0987	-0.0893	-0.4984	-0.0745	-0.0454	-0.0528	0.333	0.1293	0.1122	0.1764	0.0573	0.0524	0.1445	0.0195	0.2149	36.1715	-33.5656	-12.7854
13	4.6704	0.1361	-0.1401	1.1022	0.2777	0.5518	-0.038	-0.2982	-0.2845	0.0819	-0.0064	-0.0078	0.0645	-0.068	0.0271	0.1582	0.0317	0.0153	0.1258	0.0112	0.0972	26.0296	-23.4311	-7.341
14	2.2007	0.2828	0.1128	1.2247	-0.0852	1.2034	-0.0055	0.1419	0.2283	-0.1427	-0.003	-0.0292	-0.0994	-0.0336	0.0144	0.1209	0.041	0.0215	0.1041	0.0183	0.0985	27.3312	-18.5464	-15.0432
15	6.0061	-1.5301	1.894	2.2572	-1.6038	3.3342	0.3772	0.4071	0.2965	-0.4382	-0.2315	-0.1134	0.0474	-0.0092	-0.2317	0.1586	0.0741	0.0614	0.168	0.037	0.1308	34.9541	-17.5142	-20.2525
16	4.0193	0.9395	3.5032	5.1115	2.3441	8.2443	-0.159	0.3064	0.7373	-0.3838	0.1467	0.018	-0.9561	-0.3903	0.2286	0.3259	0.1275	0.0541	0.296	0.1624	0.329	27.8646	-9.1293	-23.4761
17	3.2765	-0.2984	1.0273	2.8207	-0.3534	3.113	-0.178	-0.2662	0.4226	0.8467	-0.1341	-0.3473	-0.3178	-0.0709	0.1512	0.5139	-0.0261	-0.043	0.1392	-0.015	0.262	43.2656	4.6239	13.3197
18	1.3637	-0.3403	0.0931	3.5634	0.6317	1.5391	-0.0695	0.069	0.0639	-0.1392	-0.0317	-0.0808	-0.2888	-0.0082	0.0947	0.2302	-0.0272	0.01	0.1118	0.0561	0.1578	41.0057	1.4233	-2.9092
19	0.865	0.4218	-0.1842	4.3944	-0.1431	0.8373	0.0683	-0.0006	0.1107	0.1361	-0.125	-0.5156	-0.0779	0.1551	0.029	0.2037	-0.0269	-0.0172	0.1312	0.0557	0.2384	48.7244	-4.7518	1.2661
20	2.1033	-0.2361	0.6581	2.2508	0.2552	1.8192	-0.0356	-0.213	0.0591	0.6452	-0.0568	-0.2493	-0.0216	0.0113	0.002	0.3263	-0.0235	-0.0176	0.1365	0.054	0.1773	44.0433	-9.5366	9.9452
21	3.0959	0.5131	-1.6294	2.419	-1.0272	3.6367	-0.0848	-0.5333	0.203	1.3215	0.0292	-0.1356	-0.3665	0.0313	0.0145	0.6234	-0.0782	-0.0633	0.2221	0.0059	0.1488	43.3717	-1.7324	18.1074
22	1.9841	-0.1573	0.9458	1.1701	0.4321	0.6673	0.3238	0.2352	0.1208	-0.4152	0.4747	-0.7735	-0.2829	0.6125	-0.0764	0.3353	-0.1859	0.1723	0.3143	-0.1493	0.8606	19.0905	-43.3207	-9.2271
23	2.6589	1.4263	-1.8408	0.8175	-1.0676	1.9736	0.3301	0.3445	-0.0101	-0.5927	0.0268	-0.2234	0.0267	0.1215	-0.0131	0.4723	-0.0502	0.1013	0.1554	0.0594	0.5022	10.9349	-37.9358	-9.346
24	2.9387	1.0235	-0.4448	3.4251	0.3905	1.4311	0.2407	-0.2455	0.2737	0.0748	-0.0925	-0.273	-0.4055	-0.0212	-0.0895	0.3235	-0.0345	-0.0557	0.144	-0.0004	0.263	2.8673	-36.2961	1.1287
25	1.2379	-0.4625	-0.3865	3.0945	0.6068	1.1123	0.1226	0.0182	0.0994	-0.1268	-0.1028	-0.3061	-0.1241	0.0307	-0.0288	0.3146	-0.0434	-0.043	0.1293	0.0243	0.2549	3.8239	-46.7383	-4.5563
26	2.43	-0.016	-0.6772	4.012	-1.2014	2.1051	0.2002	-0.0127	0.0272	-0.408	0.1393	-0.9522	-0.433	0.2816	-0.2652	0.3631	-0.0215	0.0766	0.1211	0.0016	0.4585	11.8517	-50.622	-9.1482
27	3.4586	1.8236	2.7486	2.9591	1.0759	4.1403	-0.019	0.2714	-0.2255	-0.1251	0.2026	-1.2821	0.2864	1.0932	-0.1498	0.2574	0.0324	0.0331	0.4129	-0.1657	0.9583	21.6223	-54.5532	-8.1382

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 31 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 32 through 40 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 41 through 68 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 69 through 99 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 100 through 107 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 108 through 120 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 121 through 145 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 146 through 160 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 13 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 14 through 40 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 41 through 68 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 69 through 99 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 100 through 134 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 135 through 145 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 146 through 160 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1 through 13 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 14 through 54 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 55 through 106 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 107 through 134 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 135 through 160 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1 through 13 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 14 through 22 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 23 through 54 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 55 through 120 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 121 through 145 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 146 through 160 )

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