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- PDB-4wzn: CRYSTAL STRUCTURE OF THE 2B PROTEIN SOLUBLE DOMAIN FROM HEPATITIS... -

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Basic information

Entry
Database: PDB / ID: 4wzn
TitleCRYSTAL STRUCTURE OF THE 2B PROTEIN SOLUBLE DOMAIN FROM HEPATITIS A VIRUS
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / FIBER / VIRAL RECRUITMENT MACHINERY / HEPATITIS A VIRUS / NON-STRUCTURAL PROTEIN
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid ...: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHuman hepatitis A virus genotype IB
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsGarriga, D. / Vives-Adrian, L. / Buxaderas, M. / Ferreira-da-Silva, F. / Almeida, B. / Macedo-Ribeiro, S. / Pereira, P.J. / Verdaguer, N.
Citation
Journal: J.Virol. / Year: 2015
Title: Structural Basis for Host Membrane Remodeling Induced by Protein 2B of Hepatitis A Virus.
Authors: Vives-Adrian, L. / Garriga, D. / Buxaderas, M. / Fraga, J. / Pereira, P.J. / Macedo-Ribeiro, S. / Verdaguer, N.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2011
Title: CLONING, PURIFICATION AND PRELIMINARY CRYSTALLOGRAPHIC STUDIES OF THE 2AB PROTEIN FROM HEPATITIS A VIRUS.
Authors: Garriga, D. / Vives-Adrian, L. / Buxaderas, M. / Ferreira-Da-Silva, F. / Almeida, B. / Macedo-Ribeiro, S. / Pereira, P.J. / Verdaguer, N.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4764
Polymers50,2922
Non-polymers1842
Water45025
1
A: Genome polyprotein
B: Genome polyprotein
hetero molecules
x 5


Theoretical massNumber of molelcules
Total (without water)252,37920
Polymers251,45810
Non-polymers92110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z+1/21
crystal symmetry operation2_664-x+1,-y+1,z-1/21
crystal symmetry operation3_654-y+1,x,z-1/41
crystal symmetry operation4_565y,-x+1,z+1/41
2


  • Idetical with deposited unit
  • defined by software
  • DIMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-12 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.420, 90.420, 73.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Genome polyprotein


Mass: 25145.840 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 765-981
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human hepatitis A virus genotype IB (isolate HM175)
Strain: isolate HM175 / Plasmid: PTYB1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P08617, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1M MES PH5.2-5.8, 1.26M AMMONIUM SULFATE, 5MM DTT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
PH range: 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2010
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.7→90.536 Å / Num. obs: 13240 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 73.71 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 8.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.273 / % possible all: 62.9

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.22 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.213 821 6.2 %RANDOM
Rwork0.182 ---
obs0.184 13239 100 %-
Displacement parametersBiso mean: 69.32 Å2
Baniso -1Baniso -2Baniso -3
1--2.2089 Å20 Å20 Å2
2---2.2089 Å20 Å2
3---4.4179 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 12 25 2292
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012325HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.133134HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d827SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes333HARMONIC5
X-RAY DIFFRACTIONt_it2325HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion20.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3134HARMONIC2
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.7→2.92 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2936 145 6.91 %
Rwork0.2225 1953 -
all0.2276 2098 -
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)
10.63012.0159-0.366410.1436-2.00330.6507-0.02310.08760.3822-0.69760.0760.8149-0.3258-0.1196-0.05290.15440.0279-0.0533-0.29290.0265-0.020640.641770.142336.9237
210.87950.9747-2.98251.5022-0.4743.716-0.1482-0.183-0.60760.08120.01150.25480.1705-0.45360.1366-0.2989-0.04340.0461-0.0197-0.0525-0.143521.688940.807154.4538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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