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- PDB-7i1q: PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2... -

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Basic information

Entry
Database: PDB / ID: 7i1q
TitlePanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with MFP-0011753-001-001
Components
  • Serine protease NS3
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / SGC - Diamond I04-1 / PanDDA / XChemExplorer
Function / homology
Function and homology information


symbiont-mediated suppression of host interferon-mediated signaling pathway / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / viral capsid / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host toll-like receptor signaling pathway ...symbiont-mediated suppression of host interferon-mediated signaling pathway / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / viral capsid / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / protein-macromolecule adaptor activity / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / viral RNA genome replication / serine-type endopeptidase activity / DNA clamp loader activity / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / : / viral envelope / host cell nucleus / GTP binding / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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 / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsNi, X. / Marples, P.G. / Godoy, A.S. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Fairhead, M. / Lithgo, R.M. / Balaji, G. / Phelps, J. ...Ni, X. / Marples, P.G. / Godoy, A.S. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Fairhead, M. / Lithgo, R.M. / Balaji, G. / Phelps, J. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Williams, E.P. / Chandran, A.V. / Walsh, M.A. / Fearon, D. / von Delft, F.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)IC180100021 Australia
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Ni, X. / Marples, P.G. / Godoy, A.S. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Fairhead, M. / Lithgo, R.M. / Balaji, G. / Phelps, J. / Thompson, W. / Tomlinson, C.W.E. / Wild, ...Authors: Ni, X. / Marples, P.G. / Godoy, A.S. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Fairhead, M. / Lithgo, R.M. / Balaji, G. / Phelps, J. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Williams, E.P. / Chandran, A.V. / Walsh, M.A. / Fearon, D. / von Delft, F.
History
DepositionFeb 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease subunit NS2B
B: Serine protease NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7397
Polymers23,1852
Non-polymers5545
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.544, 42.544, 216.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-322-

HOH

21B-366-

HOH

31B-370-

HOH

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Components

#1: Protein/peptide Serine protease subunit NS2B / Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B


Mass: 5067.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q32ZE1
#2: Protein Serine protease NS3 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 18117.629 Da / Num. of mol.: 1 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-A1BXJ / ethyl 4-amino-8-cyanoquinoline-3-carboxylate


Mass: 241.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 30% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.73→216.75 Å / Num. obs: 22079 / % possible obs: 100 % / Redundancy: 25.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.036 / Rrim(I) all: 0.182 / Χ2: 0.27 / Net I/σ(I): 9.2 / Num. measured all: 560753
Reflection shellResolution: 1.73→1.76 Å / % possible obs: 99.2 % / Redundancy: 25.6 % / Num. measured all: 31616 / Num. unique obs: 1235 / CC1/2: 0.189 / Rpim(I) all: 2.703 / Rrim(I) all: 13.776 / Χ2: 0.13 / Net I/σ(I) obs: 0.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→54.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.42 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31252 896 4.9 %RANDOM
Rwork0.24826 ---
obs0.25147 17327 83.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.589 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å2-0 Å2-0 Å2
2--2.38 Å20 Å2
3----4.75 Å2
Refinement stepCycle: 1 / Resolution: 1.73→54.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 34 95 1605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0142099
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151734
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.6362552
X-RAY DIFFRACTIONr_angle_other_deg1.1831.5914010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4265250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84122.77183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6415298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.311510
X-RAY DIFFRACTIONr_chiral_restr0.0510.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022203
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4125.3511058
X-RAY DIFFRACTIONr_mcbond_other3.4625.2981025
X-RAY DIFFRACTIONr_mcangle_it5.37.8311206
X-RAY DIFFRACTIONr_mcangle_other5.2997.8361207
X-RAY DIFFRACTIONr_scbond_it3.8995.8471041
X-RAY DIFFRACTIONr_scbond_other3.8975.8511042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2388.3971347
X-RAY DIFFRACTIONr_long_range_B_refined9.0258.3442044
X-RAY DIFFRACTIONr_long_range_B_other8.97858.1632027
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.731→1.776 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 9 -
Rwork0.601 167 -
obs--11.03 %

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