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- PDB-8ulj: Prefusion RSV F bound by neutralizing antibody 2E08 -

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Basic information

Entry
Database: PDB / ID: 8ulj
TitlePrefusion RSV F bound by neutralizing antibody 2E08
Components
  • 2E08 Fab Heavy Chain
  • 2E08 Fab Light Chain
  • Fusion glycoprotein F0,Fibritin
  • Fusion glycoprotein F2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / RSV / antibody / neutralizing / prefusion / antiviral / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Translation of respiratory syncytial virus mRNAs / symbiont-mediated induction of syncytium formation / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / virion component / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell ...Translation of respiratory syncytial virus mRNAs / symbiont-mediated induction of syncytium formation / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / virion component / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0 / Fibritin
Similarity search - Component
Biological speciesRespiratory syncytial virus A2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHarshbarger, W.D. / Andreano, E. / Malito, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Structural and functional properties of monoclonal and vaccine-induced antibodies targeting epitopes of emerging RSV variants
Authors: Xian, Y. / Andreano, E. / Tian, S. / Phung, E. / Garbinski, L. / Biancucci, M. / Lofano, G. / Mallett, C.P. / Balsaraf, A. / Huang, Y. / Buricchi, F. / Finco, O. / Rappuoli, R. / Bottomley, ...Authors: Xian, Y. / Andreano, E. / Tian, S. / Phung, E. / Garbinski, L. / Biancucci, M. / Lofano, G. / Mallett, C.P. / Balsaraf, A. / Huang, Y. / Buricchi, F. / Finco, O. / Rappuoli, R. / Bottomley, M.J. / Chandramouli, S. / Warter, L. / Williams, J. / Malito, E. / Harshbarger, W.D.
History
DepositionOct 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F2
L: 2E08 Fab Light Chain
H: 2E08 Fab Heavy Chain
B: Fusion glycoprotein F0,Fibritin


Theoretical massNumber of molelcules
Total (without water)103,7384
Polymers103,7384
Non-polymers00
Water00
1
A: Fusion glycoprotein F2
L: 2E08 Fab Light Chain
H: 2E08 Fab Heavy Chain
B: Fusion glycoprotein F0,Fibritin

A: Fusion glycoprotein F2
L: 2E08 Fab Light Chain
H: 2E08 Fab Heavy Chain
B: Fusion glycoprotein F0,Fibritin

A: Fusion glycoprotein F2
L: 2E08 Fab Light Chain
H: 2E08 Fab Heavy Chain
B: Fusion glycoprotein F0,Fibritin


Theoretical massNumber of molelcules
Total (without water)311,21412
Polymers311,21412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)164.715, 164.715, 146.157
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

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Components

#1: Protein Fusion glycoprotein F2 / F2


Mass: 8873.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus A2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P03420
#2: Antibody 2E08 Fab Light Chain


Mass: 23336.850 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: Antibody 2E08 Fab Heavy Chain


Mass: 25919.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal TEV cleavage site and 6 x His tag / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Protein Fusion glycoprotein F0,Fibritin / Collar protein / Whisker antigen control protein


Mass: 45609.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fibritin trimerization domain fused to C terminus of RSV glycoprotein F1 domain,Fibritin trimerization domain fused to C terminus of RSV glycoprotein F1 domain
Source: (gene. exp.) Respiratory syncytial virus A2 / Gene: wac / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A088S9A7, UniProt: P10104
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: 5.52 Å3/Da / Density % sol: 77.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 23.64%w/v PEG 1500, 0.1 M MMT buffer (DL-malic acid:MES:Tris base at a molar ratio of 1:2:2) with pH 4.36

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→43.39 Å / Num. obs: 45920 / % possible obs: 98.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 68.2 Å2 / CC1/2: 0.98 / Net I/σ(I): 16
Reflection shellResolution: 3→3.108 Å / Num. unique obs: 4550 / CC1/2: 0.952

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→43.39 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 1982 4.36 %
Rwork0.237 --
obs0.2382 45465 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→43.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6894 0 0 0 6894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d5.24969
X-RAY DIFFRACTIONf_chiral_restr0.0431130
X-RAY DIFFRACTIONf_plane_restr0.0051218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.3841390.31293063X-RAY DIFFRACTION99
3.08-3.160.33881400.29013082X-RAY DIFFRACTION99
3.16-3.250.31631370.27833078X-RAY DIFFRACTION98
3.25-3.360.29751410.28743062X-RAY DIFFRACTION98
3.36-3.480.28051420.26423048X-RAY DIFFRACTION98
3.48-3.620.30581320.25873047X-RAY DIFFRACTION97
3.62-3.780.28151310.25892903X-RAY DIFFRACTION93
3.78-3.980.29471440.2573087X-RAY DIFFRACTION99
3.98-4.230.23391420.22483167X-RAY DIFFRACTION100
4.23-4.560.20971420.20183151X-RAY DIFFRACTION100
4.56-5.010.19431460.2063167X-RAY DIFFRACTION100
5.01-5.740.28781480.22853148X-RAY DIFFRACTION100
5.74-7.220.28531470.25373169X-RAY DIFFRACTION99
7.23-43.390.2441510.20663311X-RAY DIFFRACTION99

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