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- PDB-6ol5: Structure of iglb12 Fab in complex with anti-idiotype ib3 Fab -

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Basic information

Entry
Database: PDB / ID: 6ol5
TitleStructure of iglb12 Fab in complex with anti-idiotype ib3 Fab
Components
  • ib3 Heavy Chain
  • ib3 Light Chain
  • iglb12 Heavy Chain
  • iglb12 Light Chain
KeywordsIMMUNE SYSTEM / glb12 / Antibody / ib3 / Fab / complex / Anti-Idiotype / HIV / Broadly Neutralizing
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / AMMONIUM ION / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWeidle, C. / Pancera, 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 2.0Dec 18, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Oct 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
Revision 2.2Oct 9, 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: ib3 Heavy Chain
B: ib3 Light Chain
H: iglb12 Heavy Chain
L: iglb12 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,88051
Polymers95,5284
Non-polymers2,35247
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size exclusion chromatography was used to purify the complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.551, 75.551, 389.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Antibody , 4 types, 4 molecules ABHL

#1: Antibody ib3 Heavy Chain


Mass: 23883.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody ib3 Light Chain


Mass: 23689.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody iglb12 Heavy Chain


Mass: 24527.486 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: 23427.906 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 , 5 types, 255 molecules

#5: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, and 50%(+/-) 2-methyl-2,4-pentanediol

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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 6M / Detector: PIXEL / Date: Aug 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 26152 / % possible obs: 99.5 % / Redundancy: 17.7 % / Net I/σ(I): 10.3
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 1174 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Cootmodel building
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HZH

1hzh


Resolution: 2.9→49.408 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1351 5.19 %
Rwork0.1995 --
obs0.2021 26032 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 117 208 6915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036828
X-RAY DIFFRACTIONf_angle_d0.6249304
X-RAY DIFFRACTIONf_dihedral_angle_d14.6322457
X-RAY DIFFRACTIONf_chiral_restr0.0441027
X-RAY DIFFRACTIONf_plane_restr0.0031176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8997-3.00340.30811280.26812179X-RAY DIFFRACTION91
3.0034-3.12360.28571560.25282391X-RAY DIFFRACTION99
3.1236-3.26570.3061280.22642441X-RAY DIFFRACTION100
3.2657-3.43790.29661360.21472450X-RAY DIFFRACTION100
3.4379-3.65320.30571380.18522423X-RAY DIFFRACTION100
3.6532-3.93510.23811300.18452490X-RAY DIFFRACTION100
3.9351-4.33090.19541350.14742467X-RAY DIFFRACTION100
4.3309-4.95710.17891410.1422510X-RAY DIFFRACTION100
4.9571-6.24350.23411190.19692588X-RAY DIFFRACTION100
6.2435-49.41490.27741400.25812742X-RAY DIFFRACTION100

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