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- PDB-6vrq: Crystal structure of gl12A21 Fab in complex with anti-idiotypic i... -

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Basic information

Entry
Database: PDB / ID: 6vrq
TitleCrystal structure of gl12A21 Fab in complex with anti-idiotypic iv12 Fab
Components
  • gl12A21 Fab Heavy Chain
  • gl12A21 Fab Light Chain
  • iv12 Fab Heavy Chain
  • iv12 Fab Light Chain
KeywordsIMMUNE SYSTEM / Fab / Complex / gl12A21 / HIV / CD4-binding site / iv12
Function / homology: / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsAljedani, S.S. / Weidle, C. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2021
Title: Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies.
Authors: Seydoux, E. / Wan, Y.H. / Feng, J. / Wall, A. / Aljedani, S. / Homad, L.J. / MacCamy, A.J. / Weidle, C. / Gray, M.D. / Brumage, L. / Taylor, J.J. / Pancera, M. / Stamatatos, L. / McGuire, A.T.
History
DepositionFeb 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: iv12 Fab Heavy Chain
L: iv12 Fab Light Chain
A: gl12A21 Fab Heavy Chain
B: gl12A21 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,64022
Polymers95,5684
Non-polymers1,07218
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Complex was purified from the monomeric components by SEC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.174, 202.858, 72.341
Angle α, β, γ (deg.)90.000, 93.009, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

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Antibody , 4 types, 4 molecules HLAB

#1: Antibody iv12 Fab Heavy Chain


Mass: 24004.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): 293 / Production host: Homo sapiens (human)
#2: Antibody iv12 Fab Light Chain


Mass: 23410.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): 293 / Production host: Homo sapiens (human)
#3: Antibody gl12A21 Fab Heavy Chain


Mass: 25232.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 293 / Production host: Homo sapiens (human)
#4: Antibody gl12A21 Fab Light Chain


Mass: 22920.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 293 / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 350 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M KCl 0.1M Tris pH 8 15%w/v PEG MME 2K

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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 PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→36.12 Å / Num. obs: 34290 / % possible obs: 99.7 % / Redundancy: 2.66 % / Biso Wilson estimate: 41.75 Å2 / CC1/2: 0.997 / Net I/σ(I): 21.98
Reflection shellResolution: 2.574→2.66 Å / Num. unique obs: 2332 / CC1/2: 0.638

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Processing

Software
NameVersionClassification
Coot1.17.1_3660model building
PHENIX1.17.1_3660refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6mft

6mft


Resolution: 2.57→36.12 Å / SU ML: 0.3395 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.241 1764 5.14 %
Rwork0.1886 32526 -
obs0.1913 34290 92.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.18 Å2
Refinement stepCycle: LAST / Resolution: 2.57→36.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6382 0 57 332 6771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066618
X-RAY DIFFRACTIONf_angle_d0.76449016
X-RAY DIFFRACTIONf_chiral_restr0.0471019
X-RAY DIFFRACTIONf_plane_restr0.00481162
X-RAY DIFFRACTIONf_dihedral_angle_d16.25642306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.640.3353960.25771675X-RAY DIFFRACTION61.99
2.64-2.720.3621070.24661928X-RAY DIFFRACTION72.27
2.72-2.810.34291130.23232264X-RAY DIFFRACTION84.11
2.81-2.910.26661240.22632487X-RAY DIFFRACTION92.92
2.91-3.030.26541320.22552681X-RAY DIFFRACTION98.88
3.03-3.160.26131430.23272674X-RAY DIFFRACTION99.75
3.16-3.330.30411450.21952673X-RAY DIFFRACTION99.65
3.33-3.540.24211500.20062683X-RAY DIFFRACTION99.86
3.54-3.810.26431360.18652701X-RAY DIFFRACTION100
3.81-4.190.2311600.16292668X-RAY DIFFRACTION99.93
4.2-4.80.16281310.13452717X-RAY DIFFRACTION99.93
4.8-6.040.19521780.15682661X-RAY DIFFRACTION100
6.05-36.120.24031490.19522714X-RAY DIFFRACTION99.65

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