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- PDB-7jlk: Crystal structure of glVRC01 Fab in complex with anti-idiotype iv... -

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Basic information

Entry
Database: PDB / ID: 7jlk
TitleCrystal structure of glVRC01 Fab in complex with anti-idiotype iv1 scFv
Components
  • glVRC01 Heavy Chain
  • glVRC01 Light Chain
  • iv1 Heavy Chain
  • iv1 Light Chain
KeywordsIMMUNE SYSTEM / iv1 / glVRC01 / Fab / scFv / HIV-1 / anti-idiotype
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 29, 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

Downloads & links

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Assembly

Deposited unit
H: iv1 Heavy Chain
A: glVRC01 Heavy Chain
B: glVRC01 Light Chain
L: iv1 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,32544
Polymers75,6594
Non-polymers1,66640
Water8,683482
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Complex was further purified by size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.019, 85.244, 113.636
Angle α, β, γ (deg.)90.000, 99.733, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11H-370-

HOH

21B-550-

HOH

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Components

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Antibody , 4 types, 4 molecules HABL

#1: Antibody iv1 Heavy Chain


Mass: 14582.077 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 glVRC01 Heavy Chain


Mass: 25319.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 / Production host: Homo sapiens (human)
#3: 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)
#4: Antibody iv1 Light Chain


Mass: 12738.078 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)

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Non-polymers , 5 types, 522 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Hepes pH 7.0, PEG 8000 / Temp details: room temperture

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.2 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 44594 / % possible obs: 99.15 % / Redundancy: 1.7 % / Biso Wilson estimate: 34.69 Å2 / CC1/2: 0.911 / Net I/σ(I): 4
Reflection shellResolution: 1.99→2.07 Å / Num. unique obs: 4230 / CC1/2: 0.822

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Processing

Software
NameVersionClassification
PHASER1.15.2_3472phasing
PHENIX1.15.2_3472refinement
Cootmodel building
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFT

6mft


Resolution: 1.99→42.62 Å / SU ML: 0.2474 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 2272 5.1 %
Rwork0.1791 42308 -
obs0.182 44580 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.67 Å2
Refinement stepCycle: LAST / Resolution: 1.99→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 82 482 5638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025237
X-RAY DIFFRACTIONf_angle_d0.50597102
X-RAY DIFFRACTIONf_chiral_restr0.0429783
X-RAY DIFFRACTIONf_plane_restr0.003910
X-RAY DIFFRACTIONf_dihedral_angle_d11.27943084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.30261170.26692414X-RAY DIFFRACTION90.17
2.04-2.080.31241360.27262619X-RAY DIFFRACTION98.92
2.08-2.140.29871450.242652X-RAY DIFFRACTION99.33
2.14-2.190.30151650.23662623X-RAY DIFFRACTION99.36
2.19-2.260.27621320.2342625X-RAY DIFFRACTION99.64
2.26-2.330.32691330.22382654X-RAY DIFFRACTION99.57
2.33-2.420.26681450.20482692X-RAY DIFFRACTION99.96
2.42-2.510.2911550.21212635X-RAY DIFFRACTION99.75
2.51-2.630.2761510.19612649X-RAY DIFFRACTION99.96
2.63-2.760.26861400.19892665X-RAY DIFFRACTION99.89
2.76-2.940.24741380.18922642X-RAY DIFFRACTION99.93
2.94-3.160.24611340.18592666X-RAY DIFFRACTION99.96
3.16-3.480.25031490.1652672X-RAY DIFFRACTION99.93
3.48-3.990.20451430.14822682X-RAY DIFFRACTION100
3.99-5.020.16231250.13112719X-RAY DIFFRACTION100
5.02-42.620.21171640.17642699X-RAY DIFFRACTION99.72

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