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- PDB-6vlw: Crystal Structure of 426cOD in Complex with VRC01 Fab -

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Basic information

Entry
Database: PDB / ID: 6vlw
TitleCrystal Structure of 426cOD in Complex with VRC01 Fab
Components
  • 426cOD
  • VRC01 Fab Heavy Chain
  • VRC01 Fab Light Chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV / 426c / Outer Domain / VRC01 / 426cOD / FAB / CD4 / antibody / immunogen / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 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)P01 AI138212 United States
CitationJournal: Immunity / Year: 2020
Title: HIV-1 VRC01 Germline-Targeting Immunogens Select Distinct Epitope-Specific B Cell Receptors.
Authors: Lin, Y.R. / Parks, K.R. / Weidle, C. / Naidu, A.S. / Khechaduri, A. / Riker, A.O. / Takushi, B. / Chun, J.H. / Borst, A.J. / Veesler, D. / Stuart, A. / Agrawal, P. / Gray, M. / Pancera, M. / ...Authors: Lin, Y.R. / Parks, K.R. / Weidle, C. / Naidu, A.S. / Khechaduri, A. / Riker, A.O. / Takushi, B. / Chun, J.H. / Borst, A.J. / Veesler, D. / Stuart, A. / Agrawal, P. / Gray, M. / Pancera, M. / Huang, P.S. / Stamatatos, L.
History
DepositionJan 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: VRC01 Fab Heavy Chain
L: VRC01 Fab Light Chain
G: 426cOD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,51219
Polymers69,7013
Non-polymers1,81116
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size exclusion chromatography was used to further purify the complex.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.367, 137.367, 66.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules G

#3: Protein 426cOD


Mass: 21872.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)

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Antibody , 2 types, 2 molecules HL

#1: Antibody VRC01 Fab Heavy Chain


Mass: 24726.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody VRC01 Fab Light Chain


Mass: 23102.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Sugars , 2 types, 4 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 72 molecules

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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Na
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 4.68 Å3/Da / Density % sol: 73.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18.425% PEG 3350, 11.011% 2-Methyl-2,4-pentanediol, 0.22M Lithium Sulfate, 0.11M Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.42→50 Å / Num. obs: 15995 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 63.14 Å2 / CC1/2: 0.992 / Net I/σ(I): 25.57
Reflection shellResolution: 3.42→3.48 Å / Num. unique obs: 854 / CC1/2: 0.661

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFA

5ifa


Resolution: 3.42→48.57 Å / SU ML: 0.5125 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.675
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261 775 4.85 %
Rwork0.2104 15209 -
obs0.2128 15984 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.24 Å2
Refinement stepCycle: LAST / Resolution: 3.42→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 104 60 4587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00364620
X-RAY DIFFRACTIONf_angle_d0.66316298
X-RAY DIFFRACTIONf_chiral_restr0.0493714
X-RAY DIFFRACTIONf_plane_restr0.0049821
X-RAY DIFFRACTIONf_dihedral_angle_d16.48251648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.640.3717970.27221769X-RAY DIFFRACTION66.55
3.64-3.920.28511140.24482654X-RAY DIFFRACTION99.1
3.92-4.310.26451160.19052685X-RAY DIFFRACTION100
4.31-4.930.20461320.17122685X-RAY DIFFRACTION100
4.93-6.210.21941330.19472696X-RAY DIFFRACTION100
6.21-48.570.27911830.22952720X-RAY DIFFRACTION99.62

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