PDB-4gua: Alphavirus P23pro-zbd

ID or keywords:

Entry

Database: PDB / ID: 4gua

Title

Alphavirus P23pro-zbd

Components

Non-structural polyprotein

Keywords

HYDROLASE / viral precursor polyprotein / protease / zinc-binding

Function / homology

Function and homology information

O-acetyl-ADP-ribose deacetylase activity / positive stranded viral RNA replication / host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase ...
Similarity search - Function

Biological species

Sindbis virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.854 Å

Authors

Shin, G. / Yost, S. / Miller, M. / Marcotrigiano, J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and functional insights into alphavirus polyprotein processing and pathogenesis.
Authors: Shin, G. / Yost, S.A. / Miller, M.T. / Elrod, E.J. / Grakoui, A. / Marcotrigiano, J.

History

Deposition	Aug 29, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 3, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 24, 2012	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gua.cif.gz	770.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4gua.ent.gz	647.1 KB	Display	PDB format
PDBx/mmJSON format	4gua.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4gua_validation.pdf.gz	490.5 KB	Display	wwPDB validaton report
Full document	4gua_full_validation.pdf.gz	514.2 KB	Display
Data in XML	4gua_validation.xml.gz	67.7 KB	Display
Data in CIF	4gua_validation.cif.gz	90.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/4gua ftp://data.pdbj.org/pub/pdb/validation_reports/gu/4gua	HTTPS FTP

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Related structure data

Related structure data	2hwkS 3gpgS 3gpo 3gpq 3gqo 3trk S: Starting model for refinement
Similar structure data	1i88-1 4tnd-d 1bi5-1 1oq7-1 1v3j-1 3awk-1 3wy0-d 1i89-1 1d6f-1 6dx9-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1)

Deposited unit

A: Non-structural polyprotein

B: Non-structural polyprotein

C: Non-structural polyprotein

hetero molecules

230 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Non-structural polyprotein

hetero molecules

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

2

B: Non-structural polyprotein

hetero molecules

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

3

C: Non-structural polyprotein

hetero molecules

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

Unit cell

Length a, b, c (Å)	147.180, 147.180, 360.440
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Non-structural polyprotein / Polyprotein nsP1234 / P1234 / P123 / P123' / mRNA-capping enzyme nsP1 / Non-structural protein 1 / ...Polyprotein nsP1234 / P1234 / P123 / P123' / mRNA-capping enzyme nsP1 / Non-structural protein 1 / Protease nsP2 / Non-structural protein 2 / nsP2 / Non-structural protein 3 / nsP3 / Non-structural protein 3' / nsP3' / RNA-directed RNA polymerase nsP4 / Non-structural protein 4 / nsP4 Mass: 74770.422 Da / Num. of mol.: 3 / Fragment: UNP residues 1011-1675 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sindbis virus / Strain: Toto1101 / Gene: P1234 polyprotein / Production host: Escherichia coli (E. coli) References: UniProt: P03317, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, polynucleotide 5'- ...References: UniProt: P03317, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, polynucleotide 5'-phosphatase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, nucleoside-triphosphate phosphatase, RNA helicase, RNA-directed RNA polymerase
#2: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.02 Å³/Da
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2 M ammonium sulfate, 0.1 M 2-(N-morpholino)ethane sulfonic acid (MES) (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.2824 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2010 / Details: Double silicon(111) crystal monochromator
Radiation	Monochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2824 Å / Relative weight: 1
Reflection	Resolution: 2.85→52.05 Å / Num. all: 105939 / Num. obs: 105713 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 2.85→3.01 Å / Redundancy: 10.4 % / R_merge(I) obs: 1.103 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.8_1066) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2HWK, 3GPG

2hwk

3gpg

Resolution: 2.854→48.176 Å / SU ML: 0.31 / Isotropic thermal model: isotropic / σ(F): 1.34 / Phase error: 21.84 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2173	5284	5 %
R_work	0.1863	-	-
obs	0.1879	105712	99.81 %
all	-	105938	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 64.65 Å²

Refine analyze

Luzzati coordinate error obs: 0.09 Å

Refinement step

Cycle: LAST / Resolution: 2.854→48.176 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15418	0	289	0	15707

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	16038
X-RAY DIFFRACTION	f_angle_d	1.109	21847
X-RAY DIFFRACTION	f_dihedral_angle_d	14.262	5850
X-RAY DIFFRACTION	f_chiral_restr	0.063	2415
X-RAY DIFFRACTION	f_plane_restr	0.005	2806

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 (%)
2.8541-2.8865	0.3039	180	0.2749	3342	X-RAY DIFFRACTION	99
2.8865-2.9205	0.2753	187	0.2546	3195	X-RAY DIFFRACTION	100
2.9205-2.9561	0.2865	173	0.26	3319	X-RAY DIFFRACTION	100
2.9561-2.9935	0.3359	194	0.253	3362	X-RAY DIFFRACTION	100
2.9935-3.0329	0.2727	167	0.2456	3226	X-RAY DIFFRACTION	100
3.0329-3.0744	0.3017	154	0.2415	3374	X-RAY DIFFRACTION	100
3.0744-3.1184	0.2828	194	0.2399	3280	X-RAY DIFFRACTION	100
3.1184-3.1649	0.296	195	0.2367	3278	X-RAY DIFFRACTION	100
3.1649-3.2143	0.2638	167	0.2281	3345	X-RAY DIFFRACTION	100
3.2143-3.267	0.28	171	0.2306	3339	X-RAY DIFFRACTION	100
3.267-3.3233	0.275	178	0.2171	3300	X-RAY DIFFRACTION	100
3.3233-3.3838	0.2475	190	0.2099	3261	X-RAY DIFFRACTION	100
3.3838-3.4488	0.2605	159	0.2073	3362	X-RAY DIFFRACTION	100
3.4488-3.5192	0.2106	164	0.1918	3314	X-RAY DIFFRACTION	100
3.5192-3.5957	0.2009	168	0.1814	3338	X-RAY DIFFRACTION	100
3.5957-3.6793	0.1987	183	0.1754	3362	X-RAY DIFFRACTION	100
3.6793-3.7713	0.2351	187	0.1791	3275	X-RAY DIFFRACTION	100
3.7713-3.8732	0.2149	186	0.1755	3393	X-RAY DIFFRACTION	100
3.8732-3.9871	0.1988	138	0.1685	3325	X-RAY DIFFRACTION	100
3.9871-4.1158	0.2124	145	0.1674	3386	X-RAY DIFFRACTION	100
4.1158-4.2628	0.1863	160	0.1634	3329	X-RAY DIFFRACTION	100
4.2628-4.4333	0.1846	161	0.1633	3390	X-RAY DIFFRACTION	100
4.4333-4.635	0.2044	183	0.1585	3365	X-RAY DIFFRACTION	100
4.635-4.8791	0.192	182	0.1548	3338	X-RAY DIFFRACTION	100
4.8791-5.1845	0.1985	185	0.1622	3359	X-RAY DIFFRACTION	100
5.1845-5.5842	0.1814	174	0.1736	3426	X-RAY DIFFRACTION	100
5.5842-6.1452	0.2101	186	0.1825	3382	X-RAY DIFFRACTION	100
6.1452-7.032	0.1956	192	0.188	3415	X-RAY DIFFRACTION	100
7.032-8.8506	0.1992	180	0.1737	3438	X-RAY DIFFRACTION	99
8.8506-48.1828	0.1891	201	0.1875	3610	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	0.4365	-0.0192	-0.1673	0.6041	0.2015	0.275	0.2363	-0.0141	-0.1382	-0.0449	-0.3212	-0.0874	-0.1557	-0.2099	-0.2752	0.73	0.3505	-0.0984	0.3595	-0.0624	0.3928	36.2516	83.609	72.4865
2	0.4325	-0.1773	-0.287	0.1005	0.2022	0.3761	0.1164	-0.1318	-0.0878	0.0999	-0.1096	-0.1945	-0.3425	0.0793	0.017	0.6634	0.1448	-0.0981	0.3734	0.0574	0.5701	56.0264	83.1752	79.3207
3	0.7752	-0.13	-0.3282	0.3155	0.3709	0.4735	0.0321	-0.0952	0.2298	-0.0532	-0.1079	-0.3737	-0.1816	0.1408	-0.0035	0.7202	0.1096	0.022	0.4441	0.2044	0.8239	75.5292	83.0071	72.9198
4	0.6438	0.0046	-0.2311	0.4774	-0.103	0.1326	0.1285	0.3427	-0.1389	-0.1651	-0.2797	-0.2024	-0.1355	-0.104	-0.0928	0.8225	0.3286	0.0679	0.3805	0.1086	0.4798	58.1408	81.1035	51.5773
5	0.3038	0.4662	0.1363	0.7114	0.1247	1.0072	-0.0945	0.1362	-0.1771	0.1625	-0.1468	0.4875	0.5299	-0.1514	0.0059	0.6295	0.0156	0.2317	0.5225	-0.1478	0.8957	-22.4351	61.7211	26.5104
6	0.4572	-0.2186	-0.1517	0.8708	0.6546	0.7715	-0.0868	0.095	0.1208	0.0347	-0.0337	0.1353	-0.0566	0.0263	-0.0467	0.4992	0.1838	0.0284	0.416	0.0414	0.5523	-4.2884	82.547	25.8792
7	0.6671	0.0993	-0.2374	0.5441	0.5331	0.7253	-0.1951	-0.1292	-0.0125	0.2918	0.1473	0.1085	0.19	0.1579	-0.015	0.6887	0.2861	0.0191	0.4705	-0.0054	0.5417	-3.6099	92.9353	52.1259
8	0.5429	-0.1465	0.0337	0.5367	0.4893	0.8768	-0.2248	0.0451	-0.063	0.4801	-0.0413	0.1368	0.3217	-0.2526	-0.0406	0.8723	0.1955	0.3211	0.3853	0.0628	0.6513	-19.9019	70.672	53.2434
9	0.282	-0.1145	-0.0675	0.9826	0.2346	0.5796	-0.0979	-0.0539	0.0797	0.2844	0.1311	-0.1182	-0.0767	0.0688	0.0336	0.5567	0.2828	-0.0666	0.3887	-0.0077	0.3156	36.8195	51.5041	35.5309
10	0.2792	-0.1036	0.1077	0.5902	0.3632	0.2899	-0.0542	0.0801	0.0696	0.1377	0.0459	0.0991	-0.066	-0.0809	0.0015	0.4622	0.231	-0.0249	0.5067	0.0217	0.3366	24.0931	55.7244	19.0921
11	0.5816	-0.0306	0.2483	0.4162	0.0334	0.2515	-0.08	-0.0439	-0.1046	0.092	0.0415	0.1172	0.0507	-0.0983	-0.0542	0.3641	0.1442	0.0763	0.4398	0.0154	0.3619	13.8988	38.7743	15.7246

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1012 through 1263 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1264 through 1360 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1361 through 1527 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1528 through 1673 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1012 through 1167 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1168 through 1360 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1361 through 1527 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1528 through 1673 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1012 through 1263 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1264 through 1360 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1361 through 1673 )

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