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- PDB-9pf9: X-ray crystal structure of ATX-350-2 Fab bound to Epstein-Barr vi... -

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Basic information

Entry
Database: PDB / ID: 9pf9
TitleX-ray crystal structure of ATX-350-2 Fab bound to Epstein-Barr virus glycoprotein 350
Components
  • (Fab ATX-350-2 ...) x 2
  • BLLF1
KeywordsIMMUNE SYSTEM / Viral protein / Complex / Antibody / EBV
Function / homology
Function and homology information


Herpesvirus major outer envelope glycoprotein / : / : / : / : / Herpes virus envelope glycoprotein gp350, N-terminal A domain / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
human gammaherpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.93 Å
AuthorsLang, K. / Kher, G. / Aldridge, N.T. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA285227 United States
CitationJournal: To Be Published
Title: Transgenic Mouse-Derived Human Monoclonal Antibodies Targeting EBV gp350 and gp42 Provide Basis for Therapeutic Development
Authors: Chan, C.B. / Lang, K. / Davis, A.R. / Wan, Y.H. / Aldridge, N.T. / Kher, G. / Scharffenberger, S.C. / Hardy, S.R. / Iureniev, R. / Giltiay, N.V. / Edwards, K.R. / Radtke, S. / Kiem, H.P. / ...Authors: Chan, C.B. / Lang, K. / Davis, A.R. / Wan, Y.H. / Aldridge, N.T. / Kher, G. / Scharffenberger, S.C. / Hardy, S.R. / Iureniev, R. / Giltiay, N.V. / Edwards, K.R. / Radtke, S. / Kiem, H.P. / Pancera, M. / McGuire, A.
History
DepositionJul 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab ATX-350-2 light chain
H: Fab ATX-350-2 heavy chain
G: BLLF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4725
Polymers97,8263
Non-polymers6462
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-19 kcal/mol
Surface area38220 Å2
Unit cell
Length a, b, c (Å)116.675, 116.675, 200.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab ATX-350-2 light chain


Mass: 23327.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pTT3 / Cell (production host): Epithelial-like / Cell line (production host): HEK293S / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): KIDNEY
#2: Antibody Fab ATX-350-2 heavy chain


Mass: 24017.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pTT3 / Cell (production host): Epithelial-like / Cell line (production host): HEK293S / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): KIDNEY

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Protein / Non-polymers , 2 types, 7 molecules G

#3: Protein BLLF1


Mass: 50481.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human gammaherpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Gene: BLLF1 / Plasmid: pTT3 / Cell (production host): Epithelial-like / Cell line (production host): HEK293-EBNA1-6E / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): KIDNEY / References: UniProt: A0A0C7T6S7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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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Details

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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Sodium Citrate:HCl pH 5. 3.15 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2024
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal SI(111) Rh/Pt coated Si
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 3.928→46.26 Å / Num. obs: 12880 / % possible obs: 99.73 % / Redundancy: 12.7 % / Biso Wilson estimate: 154.86 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.328 / Rpim(I) all: 0.129 / Rrim(I) all: 0.341 / Net I/σ(I): 9.7
Reflection shellResolution: 3.93→4.32 Å / Rmerge(I) obs: 1.695 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3126 / CC1/2: 0.689 / Rpim(I) all: 0.689 / Rrim(I) all: 1.767

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Processing

Software
NameVersionClassification
PHENIX2.0_5793refinement
XDSdata reduction
Aimless0.8.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.93→46.26 Å / SU ML: 0.5409 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 31.7095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2819 624 4.84 %
Rwork0.2416 12256 -
obs0.2435 12880 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 154.86 Å2
Refinement stepCycle: LAST / Resolution: 3.93→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6456 0 42 6 6504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236665
X-RAY DIFFRACTIONf_angle_d0.5889109
X-RAY DIFFRACTIONf_chiral_restr0.04341054
X-RAY DIFFRACTIONf_plane_restr0.00951161
X-RAY DIFFRACTIONf_dihedral_angle_d11.59942416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.93-4.320.32451710.27652955X-RAY DIFFRACTION99.21
4.32-4.950.31871590.24312988X-RAY DIFFRACTION99.78
4.95-6.230.29151460.23963067X-RAY DIFFRACTION100
6.23-46.260.24591480.23113246X-RAY DIFFRACTION99.91

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