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- PDB-8vlt: Crystal structure of glycan-targeting antibody 2526 Fab bound to ... -

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Basic information

Entry
Database: PDB / ID: 8vlt
TitleCrystal structure of glycan-targeting antibody 2526 Fab bound to Mannose
Components
  • 2526 Fab Heavy Chain
  • 2526 Fab Light Chain
KeywordsIMMUNE SYSTEM / Fab / Antibody
Function / homologyalpha-D-mannopyranose
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsLindenberger, J. / Acharya, P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI165147 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI170752 United States
CitationJournal: Plos Pathog. / Year: 2024
Title: Isolation and characterization of IgG3 glycan-targeting antibodies with exceptional cross-reactivity for diverse viral families.
Authors: Vukovich, M.J. / Shiakolas, A.R. / Lindenberger, J. / Richardson, R.A. / Bass, L.E. / Barr, M. / Liu, Y. / Go, E.P. / Park, C.S. / May, A.J. / Sammour, S. / Kambarami, C. / Huang, X. / ...Authors: Vukovich, M.J. / Shiakolas, A.R. / Lindenberger, J. / Richardson, R.A. / Bass, L.E. / Barr, M. / Liu, Y. / Go, E.P. / Park, C.S. / May, A.J. / Sammour, S. / Kambarami, C. / Huang, X. / Janowska, K. / Edwards, R.J. / Mansouri, K. / Spence, T.N. / Abu-Shmais, A.A. / Manamela, N.P. / Richardson, S.I. / Leonard, S.E.W. / Gripenstraw, K.R. / Setliff, I. / Saunders, K.O. / Bonami, R.H. / Ross, T.M. / Desaire, H. / Moore, P.L. / Parks, R. / Haynes, B.F. / Sheward, D.J. / Acharya, P. / Sautto, G.A. / Georgiev, I.S.
History
DepositionJan 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 2526 Fab Heavy Chain
L: 2526 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8613
Polymers47,6802
Non-polymers1801
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-22 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.490, 68.490, 97.341
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Antibody 2526 Fab Heavy Chain


Mass: 23890.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 2526 Fab Light Chain


Mass: 23789.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 75 mM HEPES pH 7.5, 10% PEG10K, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→59.31 Å / Num. obs: 43993 / % possible obs: 99.4 % / Redundancy: 10.7 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.3
Reflection shellResolution: 1.84→1.88 Å / Rmerge(I) obs: 0.908 / Num. unique obs: 2672

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→32.45 Å / SU ML: 0.2485 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.1212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 2180 4.96 %
Rwork0.2008 41770 -
obs0.203 43950 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.25 Å2
Refinement stepCycle: LAST / Resolution: 1.84→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 12 372 3666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633376
X-RAY DIFFRACTIONf_angle_d0.89184596
X-RAY DIFFRACTIONf_chiral_restr0.0574520
X-RAY DIFFRACTIONf_plane_restr0.0065583
X-RAY DIFFRACTIONf_dihedral_angle_d14.14021207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.880.35611520.29182545X-RAY DIFFRACTION98.39
1.88-1.920.38921340.30352622X-RAY DIFFRACTION98.82
1.92-1.970.33231220.2562605X-RAY DIFFRACTION98.59
1.97-2.030.27361240.2252631X-RAY DIFFRACTION98.82
2.03-2.090.27881680.24732584X-RAY DIFFRACTION99.21
2.09-2.150.26181460.24052589X-RAY DIFFRACTION99.02
2.15-2.230.27951380.23522589X-RAY DIFFRACTION99.09
2.23-2.320.2917860.22732662X-RAY DIFFRACTION98.96
2.32-2.420.30791680.25572568X-RAY DIFFRACTION99.82
2.42-2.550.27651550.24432618X-RAY DIFFRACTION99.5
2.55-2.710.2971440.23242613X-RAY DIFFRACTION99.53
2.71-2.920.24591170.20282615X-RAY DIFFRACTION99.85
2.92-3.220.25751400.2172642X-RAY DIFFRACTION99.78
3.22-3.680.25541060.18542635X-RAY DIFFRACTION99.85
3.68-4.630.18221400.14562636X-RAY DIFFRACTION99.96
4.64-32.450.1781400.15232616X-RAY DIFFRACTION99.75

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