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- PDB-7jln: Crystal structure of glVRC01 Fab in complex with anti-idiotype iv9 Fab -

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Basic information

Entry
Database: PDB / ID: 7jln
TitleCrystal structure of glVRC01 Fab in complex with anti-idiotype iv9 Fab
Components
  • glVRC01 Heavy Chain
  • glVRC01 Light Chain
  • iv9 Heavy Chain
  • iv9 Light Chain
KeywordsIMMUNE SYSTEM / iv9 / glVRC01 / Fab / HIV-1 / anti-idiotype
Function / homologyAMMONIUM ION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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) 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
DepositionJul 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation
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
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: iv9 Heavy Chain
B: iv9 Light Chain
H: glVRC01 Heavy Chain
L: glVRC01 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,63111
Polymers96,5004
Non-polymers1317
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, complex was further purified on size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.420, 50.073, 125.171
Angle α, β, γ (deg.)90.000, 93.103, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Antibody , 4 types, 4 molecules ABHL

#1: Antibody iv9 Heavy Chain


Mass: 24209.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody iv9 Light Chain


Mass: 23969.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody glVRC01 Heavy Chain


Mass: 25302.238 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 glVRC01 Light Chain


Mass: 23019.514 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 , 3 types, 242 molecules

#5: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.08 M Sodium Acetate, 24% PEG 4000, 0.16 M Ammonium Acetate

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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: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 26793 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 42.94 Å2 / CC1/2: 0.981 / Net I/σ(I): 7.92
Reflection shellResolution: 2.573→2.665 Å / Num. unique obs: 2057 / CC1/2: 0.676

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Processing

Software
NameVersionClassification
Coot1.15.2_3472model building
PHENIX1.15.2_3472refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFT

6mft


Resolution: 2.57→47.72 Å / SU ML: 0.3869 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.5844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2557 1294 4.83 %
Rwork0.1969 25490 -
obs0.1998 26784 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.95 Å2
Refinement stepCycle: LAST / Resolution: 2.57→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6549 0 7 235 6791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256708
X-RAY DIFFRACTIONf_angle_d0.58249131
X-RAY DIFFRACTIONf_chiral_restr0.04361018
X-RAY DIFFRACTIONf_plane_restr0.00321171
X-RAY DIFFRACTIONf_dihedral_angle_d16.79062423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.680.37991320.27542210X-RAY DIFFRACTION75.99
2.68-2.80.32911390.26042775X-RAY DIFFRACTION96.24
2.8-2.950.33841610.25662870X-RAY DIFFRACTION99.21
2.95-3.130.32331350.24712925X-RAY DIFFRACTION99.67
3.13-3.370.30491770.21482868X-RAY DIFFRACTION99.87
3.37-3.710.27111200.18452935X-RAY DIFFRACTION99.45
3.71-4.250.22771310.16552941X-RAY DIFFRACTION99.87
4.25-5.350.17091390.14872962X-RAY DIFFRACTION99.45
5.35-47.720.22461600.2013004X-RAY DIFFRACTION98.97

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