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- PDB-6j5d: Complex structure of MAb 4.2-scFv with louping ill virus envelope... -

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Basic information

Entry
Database: PDB / ID: 6j5d
TitleComplex structure of MAb 4.2-scFv with louping ill virus envelope protein Domain III
Components
  • Envelope
  • antibody heavy chain
  • antibody light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / protective and neutralizing antibody / flavivirus envelope protein / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


protein dimerization activity / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor 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 ...Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor 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 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesLouping ill virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYang, X. / Qi, J. / Peng, R. / Dai, L. / Gould, E.A. / Tien, P. / Gao, G.F.
CitationJournal: J. Virol. / Year: 2019
Title: Molecular Basis of a Protective/Neutralizing Monoclonal Antibody Targeting Envelope Proteins of both Tick-Borne Encephalitis Virus and Louping Ill Virus.
Authors: Yang, X. / Qi, J. / Peng, R. / Dai, L. / Gould, E.A. / Gao, G.F. / Tien, P.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 22, 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 1.4Nov 20, 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: Envelope
H: antibody heavy chain
L: antibody light chain


Theoretical massNumber of molelcules
Total (without water)36,1243
Polymers36,1243
Non-polymers00
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-16 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.598, 95.320, 100.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

21L-275-

HOH

31L-302-

HOH

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Components

#1: Protein Envelope


Mass: 10977.397 Da / Num. of mol.: 1 / Fragment: Domain III
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Louping ill virus / Gene: envelope
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O40970
#2: Antibody antibody heavy chain


Mass: 13169.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Antibody antibody light chain


Mass: 11977.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na HEPES pH 7.5, 1.6M K/Na phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 42003 / % possible obs: 99.7 % / Redundancy: 13.1 % / Biso Wilson estimate: 25.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4127 / CC1/2: 0.949 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVB

1svb


Resolution: 1.8→40.261 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.77
RfactorNum. reflection% reflection
Rfree0.1889 1836 4.44 %
Rwork0.1699 --
obs0.1707 41382 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 0 408 2888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112562
X-RAY DIFFRACTIONf_angle_d1.0283488
X-RAY DIFFRACTIONf_dihedral_angle_d15.713919
X-RAY DIFFRACTIONf_chiral_restr0.059375
X-RAY DIFFRACTIONf_plane_restr0.006448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7994-1.8480.2191170.20482664X-RAY DIFFRACTION87
1.848-1.90240.22711270.20912833X-RAY DIFFRACTION92
1.9024-1.96380.23821320.19573026X-RAY DIFFRACTION99
1.9638-2.0340.20991140.18993128X-RAY DIFFRACTION100
2.034-2.11540.22761360.18653048X-RAY DIFFRACTION100
2.1154-2.21170.19491310.1733073X-RAY DIFFRACTION100
2.2117-2.32830.20891450.17473100X-RAY DIFFRACTION100
2.3283-2.47420.20841550.18713019X-RAY DIFFRACTION99
2.4742-2.66520.20691900.1853041X-RAY DIFFRACTION100
2.6652-2.93330.18591480.17663091X-RAY DIFFRACTION100
2.9333-3.35760.18571350.16633148X-RAY DIFFRACTION100
3.3576-4.22940.18251280.14843151X-RAY DIFFRACTION100
4.2294-40.27070.14671780.14783224X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.8781 Å / Origin y: 15.6949 Å / Origin z: 31.6553 Å
111213212223313233
T0.0996 Å2-0.0422 Å2-0.0027 Å2-0.1205 Å20.0126 Å2--0.1029 Å2
L0.0584 °2-0.0041 °20.0429 °2-0.5042 °20.0343 °2--0.4414 °2
S-0.0079 Å °0.0088 Å °0.0091 Å °0.0163 Å °0.0134 Å °0.0102 Å °-0.0741 Å °0.0589 Å °0.0305 Å °
Refinement TLS groupSelection details: all

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