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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: Cell Rep Med / Year: 2026
Title: Transgenic mouse-derived human monoclonal antibodies targeting EBV gp350 and gp42 provide basis for therapeutic development.
Authors: Crystal B Chhan / Kevin Lang / Amelia R Davis / Yu-Hsin Wan / Nicholas T Aldridge / Gargi Kher / Samuel C Scharffenberger / Samantha R Hardy / Roman Iureniev / Natalia V Giltiay / Kristina R ...Authors: Crystal B Chhan / Kevin Lang / Amelia R Davis / Yu-Hsin Wan / Nicholas T Aldridge / Gargi Kher / Samuel C Scharffenberger / Samantha R Hardy / Roman Iureniev / Natalia V Giltiay / Kristina R Edwards / Stefan Radtke / Hans-Peter Kiem / Marie Pancera / Andrew T McGuire /
Abstract: Epstein-Barr virus (EBV) causes infectious mononucleosis and contributes to neurodegenerative disorders and malignancies, particularly in immune-compromised hosts. Transplant patients face high risk ...Epstein-Barr virus (EBV) causes infectious mononucleosis and contributes to neurodegenerative disorders and malignancies, particularly in immune-compromised hosts. Transplant patients face high risk of post-transplant lymphoproliferative disease, a life-threatening EBV-driven lymphoma. There are no EBV-specific vaccines or treatments; however, neutralizing antibodies against EBV glycoproteins may offer utility as therapeutic agents. EBV entry into B cells involves gp350, which binds complement receptors, and gp42, which engages HLA class II to trigger fusion. Most existing monoclonal antibodies (mAbs) against these antigens are non-human, limiting clinical use. Using a transgenic mouse model, we generate two gp350 and eight gp42 genetically human neutralizing mAbs that block receptor binding. Structural analyses reveal extended sites of vulnerability relevant to vaccine development. Delivery of a gp42 mAb protects humanized mice from EBV challenge, while a gp350 mAb provides partial protection. These mAbs highlight the utility of transgenic mice to produce therapeutic mAbs for preventing EBV-driven disease.
History
DepositionJul 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2026Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name

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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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