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- PDB-2ggv: Crystal structure of the West Nile virus NS2B-NS3 protease, His51... -

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Basic information

Entry
Database: PDB / ID: 2ggv
TitleCrystal structure of the West Nile virus NS2B-NS3 protease, His51Ala mutant
Components
  • non-structural protein 2B
  • non-structural protein 3
KeywordsHYDROLASE / beta barrel / serine protease / viral protease / flavivirus
Function / homology
Function and homology information


RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / symbiont-mediated suppression of host apoptosis / RNA strand annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / positive regulation of viral genome replication ...RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / symbiont-mediated suppression of host apoptosis / RNA strand annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / positive regulation of viral genome replication / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / protein-DNA complex / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / ribonucleoprotein complex / induction by virus of host autophagy / RNA-directed RNA polymerase / virus-mediated perturbation of host defense response / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Thrombin, subunit H - #120 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Thrombin, subunit H - #120 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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 / Trypsin-like serine proteases / 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 / Thrombin, subunit H / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesWest Nile virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsAleshin, A.E. / Shiryaev, S.A. / Strongin, A.Y. / Liddington, R.C.
CitationJournal: Protein Sci. / Year: 2007
Title: Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold.
Authors: Aleshin, A.E. / Shiryaev, S.A. / Strongin, A.Y. / Liddington, R.C.
History
DepositionMar 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 400COMPOUND THE PROTEINS NS2B AND NS3PRO ARE CONNECTED THROUGH A LINKER GGGGSGGGRR.
Remark 999SEQUENCE THIS IS THE LINKER SEQUENCE BETWEEN THE TWO DIFFERENT PROTEINS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: non-structural protein 2B
B: non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)26,0172
Polymers26,0172
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-20 kcal/mol
Surface area11330 Å2
MethodPISA
2
A: non-structural protein 2B
B: non-structural protein 3

A: non-structural protein 2B
B: non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)52,0344
Polymers52,0344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area7770 Å2
ΔGint-58 kcal/mol
Surface area20590 Å2
MethodPISA
3
A: non-structural protein 2B
B: non-structural protein 3

A: non-structural protein 2B
B: non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)52,0344
Polymers52,0344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area8430 Å2
ΔGint-47 kcal/mol
Surface area19930 Å2
MethodPISA
4
A: non-structural protein 2B

A: non-structural protein 2B

B: non-structural protein 3

B: non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)52,0344
Polymers52,0344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation3_564-x+y,-x+1,z-1/31
crystal symmetry operation6_554x-y,x,z-1/31
Buried area4330 Å2
ΔGint-31 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.745, 56.745, 103.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsThe biological assembly is a monomer. The H51A mutant also forms dimers in solution. The dimer is generated from the monomer in the asymmetric unit by the operation -x, -y, z.

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Components

#1: Protein non-structural protein 2B / NS2B


Mass: 5981.351 Da / Num. of mol.: 1 / Fragment: NS2B cofactor
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: Pet101/D-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: Q203W3, UniProt: P06935*PLUS
#2: Protein non-structural protein 3 / NS3


Mass: 20035.590 Da / Num. of mol.: 1 / Fragment: NS3 protease domain / Mutation: H51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: Pet101/D-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: Q203W3, UniProt: P06935*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 1500, 0.1M TRIS, 0.2M lithium cloride, 2mM mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 12.3.111
SYNCHROTRONNSLS X26C20.9779, 0.9785, 0.960
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 20, 2005
ADSC QUANTUM 42CCDOct 10, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97791
30.97851
40.961
ReflectionResolution: 1.8→49.15 Å / Num. all: 17285 / Num. obs: 17285 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2481 / Rsym value: 0.6 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
MOSFLMdata reduction
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→49.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.198 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.228 906 5.2 %RANDOM
Rwork0.191 ---
all0.193 17557 --
obs0.193 17282 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.717 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20.76 Å20 Å2
2--1.53 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 0 90 1738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221686
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9492290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06124.93577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62315274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5051510
X-RAY DIFFRACTIONr_chiral_restr0.1010.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021310
X-RAY DIFFRACTIONr_nbd_refined0.1990.2692
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.218
X-RAY DIFFRACTIONr_mcbond_it1.1091.51097
X-RAY DIFFRACTIONr_mcangle_it1.8421710
X-RAY DIFFRACTIONr_scbond_it2.4113691
X-RAY DIFFRACTIONr_scangle_it3.6484.5580
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 67 -
Rwork0.26 1205 -
obs-1272 97.55 %

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