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- PDB-7bsc: Complex structure of 1G5.3 Fab bound to DENV2 NS1c -

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Basic information

Entry
Database: PDB / ID: 7bsc
TitleComplex structure of 1G5.3 Fab bound to DENV2 NS1c
Components
  • 1G5.3 Fab Heavy Chain
  • 1G5.3 Fab Light Chain
  • Non-structural protein 1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Dengue virus / NS1 / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


virion component / extracellular region / membrane
Similarity search - Function
Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Non-structural protein 1
Similarity search - Component
Biological speciesDengue virus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 1
H: 1G5.3 Fab Heavy Chain
L: 1G5.3 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)68,6663
Polymers68,6663
Non-polymers00
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-31 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.861, 80.980, 264.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Non-structural protein 1


Mass: 20488.199 Da / Num. of mol.: 1 / Fragment: NS1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6TFL7
#2: Antibody 1G5.3 Fab Heavy Chain


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


Mass: 23772.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M DL-Malic acid pH 7.0, 12% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 39747 / % possible obs: 97.5 % / Redundancy: 12.7 % / Biso Wilson estimate: 25.11 Å2 / CC1/2: 0.99 / Net I/σ(I): 14.7
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 3632 / CC1/2: 0.992

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O6B

4o6b


Resolution: 2.31→44.32 Å / SU ML: 0.2013 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8178
RfactorNum. reflection% reflection
Rfree0.2369 1978 5.03 %
Rwork0.2054 --
obs0.207 39329 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.6 Å2
Refinement stepCycle: LAST / Resolution: 2.31→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4715 0 0 530 5245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00364840
X-RAY DIFFRACTIONf_angle_d0.6836585
X-RAY DIFFRACTIONf_chiral_restr0.2756727
X-RAY DIFFRACTIONf_plane_restr0.0038839
X-RAY DIFFRACTIONf_dihedral_angle_d22.11541768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.360.28481220.23722444X-RAY DIFFRACTION90.32
2.36-2.430.26411400.23322563X-RAY DIFFRACTION93.98
2.43-2.50.2491210.23872540X-RAY DIFFRACTION93.04
2.5-2.580.3281380.23662598X-RAY DIFFRACTION95.4
2.58-2.670.28441440.24252570X-RAY DIFFRACTION94.14
2.67-2.780.26541400.23812644X-RAY DIFFRACTION95.93
2.78-2.910.25931380.23062604X-RAY DIFFRACTION95.67
2.91-3.060.24191360.22262630X-RAY DIFFRACTION95.88
3.06-3.250.24761390.21552701X-RAY DIFFRACTION96.5
3.25-3.50.24941390.2072731X-RAY DIFFRACTION98.36
3.5-3.850.21661680.1962734X-RAY DIFFRACTION99.38
3.85-4.410.20191460.17232778X-RAY DIFFRACTION99.46
4.41-5.560.19441460.15762826X-RAY DIFFRACTION99.3
5.56-44.320.22311610.20612988X-RAY DIFFRACTION98.78
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)
10.4199409352140.0754117976543-0.3804079220390.4631862806120.09181747764771.626262683820.0210048050218-0.105932497536-0.02511792329860.1026292070380.0196878468791-0.001600084595660.01790674266880.124620090116-0.03584624586360.180068017743-0.004278254282630.001182951816110.1938058289460.008862676247160.1363888561994.93078628022-34.4313966265-20.224669013
20.336940153743-0.05978599156620.142778919850.283559976742-0.2152637017180.7154113464510.04768209423170.02349425470590.008420251359830.0318561849971-0.01080606203690.0480057181025-0.1037419546120.0579426618774-0.03274108536780.158647243354-0.00535859213930.01329955158210.127242565409-0.01742735866910.20331842808411.9799997508-13.7933351293-64.5421489665
30.2379404049680.100414295023-0.2635899266930.163905796302-0.1636111016491.045994381290.0142911368822-0.01095412036580.0437660969484-0.0227834501358-0.0172840466494-0.0127973503850.0288443445170.09000107409680.007634195048550.1598617709670.0192052302418-0.001999621917860.173581931445-0.006729873210130.22230214400525.0311848719-24.5468871519-70.9046998588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain H
3X-RAY DIFFRACTION3chain L

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