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- PDB-7bsd: Complex structure of 1G5.3 Fab bound to ZIKV NS1c -

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Basic information

Entry
Database: PDB / ID: 7bsd
TitleComplex structure of 1G5.3 Fab bound to ZIKV NS1c
Components
  • 1G5.3 Fab Heavy Chain
  • 1G5.3 Fab Light Chain
  • NS1C
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Zika virus / NS1 / antibody / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


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 / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / clathrin-dependent endocytosis of virus by host cell ...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 / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / clathrin-dependent endocytosis of virus by host cell / molecular adaptor activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / 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 / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / centrosome / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Zika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsSong, H. / Qi, J. / Gao, F.G.
CitationJournal: Science / Year: 2021
Title: A broadly protective antibody that targets the flavivirus NS1 protein.
Authors: Modhiran, N. / Song, H. / Liu, L. / Bletchly, C. / Brillault, L. / Amarilla, A.A. / Xu, X. / Qi, J. / Chai, Y. / Cheung, S.T.M. / Traves, R. / Setoh, Y.X. / Bibby, S. / Scott, C.A.P. / ...Authors: Modhiran, N. / Song, H. / Liu, L. / Bletchly, C. / Brillault, L. / Amarilla, A.A. / Xu, X. / Qi, J. / Chai, Y. / Cheung, S.T.M. / Traves, R. / Setoh, Y.X. / Bibby, S. / Scott, C.A.P. / Freney, M.E. / Newton, N.D. / Khromykh, A.A. / Chappell, K.J. / Muller, D.A. / Stacey, K.J. / Landsberg, M.J. / Shi, Y. / Gao, G.F. / Young, P.R. / Watterson, D.
History
DepositionMar 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1G5.3 Fab Heavy Chain
B: 1G5.3 Fab Light Chain
G: NS1C
I: NS1C
H: 1G5.3 Fab Heavy Chain
L: 1G5.3 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)137,8896
Polymers137,8896
Non-polymers00
Water3,513195
1
A: 1G5.3 Fab Heavy Chain
B: 1G5.3 Fab Light Chain
G: NS1C


Theoretical massNumber of molelcules
Total (without water)68,9443
Polymers68,9443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: NS1C
H: 1G5.3 Fab Heavy Chain
L: 1G5.3 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)68,9443
Polymers68,9443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.889, 111.141, 158.587
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Antibody 1G5.3 Fab Heavy Chain


Mass: 24405.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human)
#2: Antibody 1G5.3 Fab Light Chain


Mass: 23772.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein NS1C


Mass: 20766.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: A0A024B7W1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 14% v/vPoly(acrylic acid-co-maleic acid) solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.03907 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2018
Diffraction measurementDetails: 1.00 degrees, 0.2 sec, detector distance 500.00 mm / Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03907 Å / Relative weight: 1
ReflectionAv R equivalents: 0.124 / Number: 626111
ReflectionResolution: 2.5→50 Å / Num. obs: 63619 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 17.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.621 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 62455 / % possible all: 100
Cell measurementReflection used: 626111

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IY3

5iy3


Resolution: 2.53→49.5 Å / SU ML: 0.3608 / Cross valid method: FREE R-VALUE / Phase error: 25.8119
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2388 3219 5.15 %
Rwork0.2208 59236 -
obs0.2217 62455 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.73 Å2
Refinement stepCycle: LAST / Resolution: 2.53→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7701 0 0 195 7896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00337889
X-RAY DIFFRACTIONf_angle_d0.707410716
X-RAY DIFFRACTIONf_chiral_restr0.04431185
X-RAY DIFFRACTIONf_plane_restr0.00461368
X-RAY DIFFRACTIONf_dihedral_angle_d23.91352872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.570.4113680.31951329X-RAY DIFFRACTION51.19
2.57-2.610.3111940.30772269X-RAY DIFFRACTION84.76
2.61-2.660.36691400.30892474X-RAY DIFFRACTION93.89
2.66-2.70.34621480.31452530X-RAY DIFFRACTION97.7
2.7-2.750.3241290.30852638X-RAY DIFFRACTION98.82
2.75-2.80.32141730.30952580X-RAY DIFFRACTION99.57
2.8-2.860.32081540.29072618X-RAY DIFFRACTION99.78
2.86-2.920.30911420.28212644X-RAY DIFFRACTION99.82
2.92-2.990.28251450.27012629X-RAY DIFFRACTION100
2.99-3.070.29561090.2712658X-RAY DIFFRACTION100
3.07-3.150.29841350.26522631X-RAY DIFFRACTION100
3.15-3.240.28561320.26232685X-RAY DIFFRACTION100
3.24-3.350.31471430.24942633X-RAY DIFFRACTION100
3.35-3.460.27881470.252668X-RAY DIFFRACTION100
3.46-3.60.22231380.22522658X-RAY DIFFRACTION100
3.6-3.770.22611330.2072669X-RAY DIFFRACTION100
3.77-3.970.24381770.2012638X-RAY DIFFRACTION100
3.97-4.210.20021460.18612672X-RAY DIFFRACTION100
4.21-4.540.1871840.1662638X-RAY DIFFRACTION100
4.54-50.18731510.16222679X-RAY DIFFRACTION100
5-5.720.18271320.17142726X-RAY DIFFRACTION100
5.72-7.20.24161370.20152747X-RAY DIFFRACTION99.97
7.2-49.50.15821620.18012823X-RAY DIFFRACTION98.74

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