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- PDB-9pu2: Crystal structure of EEEV-179 Fab (Crystal Kappa) -

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Basic information

Entry
Database: PDB / ID: 9pu2
TitleCrystal structure of EEEV-179 Fab (Crystal Kappa)
Components
  • EEEV-179 Fab (Crystal Kappa) light chain
  • EEEV-179 Fab heavy chain
KeywordsIMMUNE SYSTEM / Fab
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBuchman, C.D. / Crowe, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2026
Title: Asymmetric structural transitions in the icosahedral organization of Eastern equine encephalitis virus.
Authors: Abhishek Bandyopadhyay / Lauren E Williamson / Cameron D Buchman / Thomas Klose / James E Crowe / Richard J Kuhn /
Abstract: Delivery of the viral genome into host cells is a critical step in successful viral infection. Alphaviruses achieve this step by fusing the viral and endosomal membranes under acidic conditions. This ...Delivery of the viral genome into host cells is a critical step in successful viral infection. Alphaviruses achieve this step by fusing the viral and endosomal membranes under acidic conditions. This process requires significant structural changes in the alphavirus glycoprotein organization. Structural characterization of acidic pH-induced conformational changes in alphavirus virions has remained elusive due to the rapid, transient nature of these states, conformational heterogeneity, and particle aggregation. Antibody binding studies conducted at elevated temperatures or under acidic pH conditions have further revealed the presence of transitional epitopes that are inaccessible on alphaviruses at room temperature or neutral pH. In this report, we present structural snapshots of the conformational changes in the glycoproteins and nucleocapsid core of a prototypical alphavirus, Eastern equine encephalitis virus, caused by exposure to 40 °C or pH 5.6. These findings provide insights into the structural transitions that occur prior to viral fusion with the endosomal membrane. This approach has also allowed us to define the molecular basis for recognition of a pan-alphavirus epitope by a patient-derived human antibody.
History
DepositionJul 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: EEEV-179 Fab (Crystal Kappa) light chain
H: EEEV-179 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,4102
Polymers48,4102
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.859, 73.106, 95.887
Angle α, β, γ (deg.)90.00, 95.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-364-

HOH

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Components

#1: Antibody EEEV-179 Fab (Crystal Kappa) light chain


Mass: 23974.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody EEEV-179 Fab heavy chain


Mass: 24435.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.3 M sodium fluoride, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 25428 / % possible obs: 97.2 % / Redundancy: 3.5 % / CC1/2: 0.982 / Net I/σ(I): 11.6
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1166 / CC1/2: 0.837 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.24 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.346 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24471 1313 5.2 %RANDOM
Rwork0.18781 ---
obs0.19068 24115 96.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.075 Å2
Baniso -1Baniso -2Baniso -3
1-3.47 Å2-0 Å22.95 Å2
2---2.94 Å2-0 Å2
3----1.06 Å2
Refinement stepCycle: 1 / Resolution: 2.25→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 0 167 3486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0113400
X-RAY DIFFRACTIONr_bond_other_d0.0090.0162981
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6454642
X-RAY DIFFRACTIONr_angle_other_deg0.5591.5526976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3925441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.873510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8410519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02654
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0665.1831773
X-RAY DIFFRACTIONr_mcbond_other5.0665.1831773
X-RAY DIFFRACTIONr_mcangle_it6.8647.7582211
X-RAY DIFFRACTIONr_mcangle_other6.8647.762212
X-RAY DIFFRACTIONr_scbond_it5.3545.4011627
X-RAY DIFFRACTIONr_scbond_other5.3525.4031628
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4077.9482432
X-RAY DIFFRACTIONr_long_range_B_refined9.67762.2183537
X-RAY DIFFRACTIONr_long_range_B_other9.7162.1773516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å
RfactorNum. reflection% reflection
Rfree0.363 80 -
Rwork0.275 1606 -
obs--88.97 %

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