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- PDB-4gua: Alphavirus P23pro-zbd -

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Basic information

Entry
Database: PDB / ID: 4gua
TitleAlphavirus P23pro-zbd
ComponentsNon-structural polyprotein
KeywordsHYDROLASE / viral precursor polyprotein / protease / zinc-binding
Function / homology
Function and homology information


negative regulation of stress granule assembly / adenylyltransferase activity / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / host cell filopodium / ADP-ribose 1''-phosphate phosphatase / polynucleotide 5'-phosphatase / mRNA methyltransferase activity / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / polynucleotide adenylyltransferase activity ...negative regulation of stress granule assembly / adenylyltransferase activity / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / host cell filopodium / ADP-ribose 1''-phosphate phosphatase / polynucleotide 5'-phosphatase / mRNA methyltransferase activity / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / polynucleotide adenylyltransferase activity / suppression by virus of host transcription / suppression by virus of host mRNA transcription via inhibition of RNA polymerase II activity / suppression by virus of host JAK-STAT cascade via inhibition of STAT1 activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / 7-methylguanosine mRNA capping / nucleoside-triphosphate phosphatase / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / positive stranded viral RNA replication / cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / RNA-directed 5'-3' RNA polymerase activity / DNA-templated transcription / suppression by virus of host type I interferon-mediated signaling pathway / GTP binding / host cell nucleus / host cell plasma membrane / ATP hydrolysis activity / RNA binding / membrane / ATP binding / metal ion binding
Similarity search - Function
Alphavirus nsP2 protease domain / Alphavirus nsP2 protease domain superfamily / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Alphavirus nsp2 protease (nsp2pro) domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / RNA dependent RNA polymerase / Tymovirus, RNA-dependent RNA polymerase ...Alphavirus nsP2 protease domain / Alphavirus nsP2 protease domain superfamily / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Alphavirus nsp2 protease (nsp2pro) domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / RNA dependent RNA polymerase / Tymovirus, RNA-dependent RNA polymerase / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Cathepsin B; Chain A / Vaccinia Virus protein VP39 / Viral (Superfamily 1) RNA helicase / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSindbis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.854 Å
AuthorsShin, G. / Yost, S. / Miller, M. / Marcotrigiano, J.
CitationJournal: 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
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural polyprotein
B: Non-structural polyprotein
C: Non-structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,72052
Polymers224,3113
Non-polymers5,40949
Water0
1
A: Non-structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,86220
Polymers74,7701
Non-polymers2,09219
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7079
Polymers74,7701
Non-polymers9368
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,15123
Polymers74,7701
Non-polymers2,38022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number152
Space group name H-MP3121

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Components

#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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.02 Å3/Da
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.2824 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2010 / Details: Double silicon(111) crystal monochromator
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.85→3.01 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.103 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1066) / Classification: refinement
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2173 5284 5 %
Rwork0.1863 --
obs0.1879 105712 99.81 %
all-105938 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.65 Å2
Refine analyzeLuzzati coordinate error obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 2.854→48.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15418 0 289 0 15707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616038
X-RAY DIFFRACTIONf_angle_d1.10921847
X-RAY DIFFRACTIONf_dihedral_angle_d14.2625850
X-RAY DIFFRACTIONf_chiral_restr0.0632415
X-RAY DIFFRACTIONf_plane_restr0.0052806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8541-2.88650.30391800.27493342X-RAY DIFFRACTION99
2.8865-2.92050.27531870.25463195X-RAY DIFFRACTION100
2.9205-2.95610.28651730.263319X-RAY DIFFRACTION100
2.9561-2.99350.33591940.2533362X-RAY DIFFRACTION100
2.9935-3.03290.27271670.24563226X-RAY DIFFRACTION100
3.0329-3.07440.30171540.24153374X-RAY DIFFRACTION100
3.0744-3.11840.28281940.23993280X-RAY DIFFRACTION100
3.1184-3.16490.2961950.23673278X-RAY DIFFRACTION100
3.1649-3.21430.26381670.22813345X-RAY DIFFRACTION100
3.2143-3.2670.281710.23063339X-RAY DIFFRACTION100
3.267-3.32330.2751780.21713300X-RAY DIFFRACTION100
3.3233-3.38380.24751900.20993261X-RAY DIFFRACTION100
3.3838-3.44880.26051590.20733362X-RAY DIFFRACTION100
3.4488-3.51920.21061640.19183314X-RAY DIFFRACTION100
3.5192-3.59570.20091680.18143338X-RAY DIFFRACTION100
3.5957-3.67930.19871830.17543362X-RAY DIFFRACTION100
3.6793-3.77130.23511870.17913275X-RAY DIFFRACTION100
3.7713-3.87320.21491860.17553393X-RAY DIFFRACTION100
3.8732-3.98710.19881380.16853325X-RAY DIFFRACTION100
3.9871-4.11580.21241450.16743386X-RAY DIFFRACTION100
4.1158-4.26280.18631600.16343329X-RAY DIFFRACTION100
4.2628-4.43330.18461610.16333390X-RAY DIFFRACTION100
4.4333-4.6350.20441830.15853365X-RAY DIFFRACTION100
4.635-4.87910.1921820.15483338X-RAY DIFFRACTION100
4.8791-5.18450.19851850.16223359X-RAY DIFFRACTION100
5.1845-5.58420.18141740.17363426X-RAY DIFFRACTION100
5.5842-6.14520.21011860.18253382X-RAY DIFFRACTION100
6.1452-7.0320.19561920.1883415X-RAY DIFFRACTION100
7.032-8.85060.19921800.17373438X-RAY DIFFRACTION99
8.8506-48.18280.18912010.18753610X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°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)
10.4365-0.0192-0.16730.60410.20150.2750.2363-0.0141-0.1382-0.0449-0.3212-0.0874-0.1557-0.2099-0.27520.730.3505-0.09840.3595-0.06240.392836.251683.60972.4865
20.4325-0.1773-0.2870.10050.20220.37610.1164-0.1318-0.08780.0999-0.1096-0.1945-0.34250.07930.0170.66340.1448-0.09810.37340.05740.570156.026483.175279.3207
30.7752-0.13-0.32820.31550.37090.47350.0321-0.09520.2298-0.0532-0.1079-0.3737-0.18160.1408-0.00350.72020.10960.0220.44410.20440.823975.529283.007172.9198
40.64380.0046-0.23110.4774-0.1030.13260.12850.3427-0.1389-0.1651-0.2797-0.2024-0.1355-0.104-0.09280.82250.32860.06790.38050.10860.479858.140881.103551.5773
50.30380.46620.13630.71140.12471.0072-0.09450.1362-0.17710.1625-0.14680.48750.5299-0.15140.00590.62950.01560.23170.5225-0.14780.8957-22.435161.721126.5104
60.4572-0.2186-0.15170.87080.65460.7715-0.08680.0950.12080.0347-0.03370.1353-0.05660.0263-0.04670.49920.18380.02840.4160.04140.5523-4.288482.54725.8792
70.66710.0993-0.23740.54410.53310.7253-0.1951-0.1292-0.01250.29180.14730.10850.190.1579-0.0150.68870.28610.01910.4705-0.00540.5417-3.609992.935352.1259
80.5429-0.14650.03370.53670.48930.8768-0.22480.0451-0.0630.4801-0.04130.13680.3217-0.2526-0.04060.87230.19550.32110.38530.06280.6513-19.901970.67253.2434
90.282-0.1145-0.06750.98260.23460.5796-0.0979-0.05390.07970.28440.1311-0.1182-0.07670.06880.03360.55670.2828-0.06660.3887-0.00770.315636.819551.504135.5309
100.2792-0.10360.10770.59020.36320.2899-0.05420.08010.06960.13770.04590.0991-0.066-0.08090.00150.46220.231-0.02490.50670.02170.336624.093155.724419.0921
110.5816-0.03060.24830.41620.03340.2515-0.08-0.0439-0.10460.0920.04150.11720.0507-0.0983-0.05420.36410.14420.07630.43980.01540.361913.898838.774315.7246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1012 through 1263 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1264 through 1360 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1361 through 1527 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1528 through 1673 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1012 through 1167 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1168 through 1360 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1361 through 1527 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1528 through 1673 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1012 through 1263 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1264 through 1360 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1361 through 1673 )

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