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- PDB-6ol6: Structure of iglb12 scFv in complex with anti-idiotype ib2 Fab -

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Basic information

Entry
Database: PDB / ID: 6ol6
TitleStructure of iglb12 scFv in complex with anti-idiotype ib2 Fab
Components
  • ib2 Heavy Chain
  • ib2 Light Chain
  • iglb12 Heavy Chain
  • iglb12 light chain
KeywordsIMMUNE SYSTEM / glb12 / Antibody / ib2 / Fab / complex / Anti-Idiotype / HIV / Neutralizing / Broadly
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWeidle, C. / Pancera, M. / Gewe, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI081625 United States
CitationJournal: J.Exp.Med. / Year: 2019
Title: Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes.
Authors: Bancroft, T. / DeBuysscher, B.L. / Weidle, C. / Schwartz, A. / Wall, A. / Gray, M.D. / Feng, J. / Steach, H.R. / Fitzpatrick, K.S. / Gewe, M.M. / Skog, P.D. / Doyle-Cooper, C. / Ota, T. / ...Authors: Bancroft, T. / DeBuysscher, B.L. / Weidle, C. / Schwartz, A. / Wall, A. / Gray, M.D. / Feng, J. / Steach, H.R. / Fitzpatrick, K.S. / Gewe, M.M. / Skog, P.D. / Doyle-Cooper, C. / Ota, T. / Strong, R.K. / Nemazee, D. / Pancera, M. / Stamatatos, L. / McGuire, A.T. / Taylor, J.J.
History
DepositionApr 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ib2 Heavy Chain
B: ib2 Light Chain
H: iglb12 Heavy Chain
L: iglb12 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8936
Polymers75,8224
Non-polymers712
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Complex was run over size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.688, 95.895, 66.741
Angle α, β, γ (deg.)90.00, 96.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-245-

HOH

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Components

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Antibody , 4 types, 4 molecules ABHL

#1: Antibody ib2 Heavy Chain


Mass: 24416.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody ib2 Light Chain


Mass: 23810.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody iglb12 Heavy Chain


Mass: 15303.977 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: Antibody iglb12 light chain


Mass: 12291.675 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 2 types, 314 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 13.4% PEG 8000, 13.4 PEG 400, 0.1 M MgCl2, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26000 / % possible obs: 99.5 % / Redundancy: 7.4 % / Net I/σ(I): 9.2
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 1171 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HZH

1hzh


Resolution: 2.6→49.105 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2306 1246 4.79 %
Rwork0.1711 --
obs0.174 25992 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→49.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5149 0 2 312 5463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025303
X-RAY DIFFRACTIONf_angle_d0.5597222
X-RAY DIFFRACTIONf_dihedral_angle_d10.5643161
X-RAY DIFFRACTIONf_chiral_restr0.044796
X-RAY DIFFRACTIONf_plane_restr0.003921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70260.29221220.21042484X-RAY DIFFRACTION90
2.7026-2.82560.28061430.21542777X-RAY DIFFRACTION100
2.8256-2.97460.33491290.21292761X-RAY DIFFRACTION100
2.9746-3.16090.2561330.19582776X-RAY DIFFRACTION100
3.1609-3.40490.27331470.19082767X-RAY DIFFRACTION100
3.4049-3.74750.23671380.16252775X-RAY DIFFRACTION100
3.7475-4.28950.19661480.14222774X-RAY DIFFRACTION100
4.2895-5.40320.15031310.12822795X-RAY DIFFRACTION100
5.4032-49.1140.22411550.18072837X-RAY DIFFRACTION100

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