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- PDB-8ulk: Prefusion RSV F bound by neutralizing antibody 1G12 -

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Basic information

Entry
Database: PDB / ID: 8ulk
TitlePrefusion RSV F bound by neutralizing antibody 1G12
Components
  • 1G12 Fab heavy chain
  • 1G12 Fab light chain
  • Fusion glycoprotein F0,Fibritin
  • Fusion glycoprotein F2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / RSV / antibody / neutralizing / pre-fusion / glycoprotein / antiviral / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / 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 / fusion of virus membrane with host plasma membrane ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / 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 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / 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 speciesHuman respiratory syncytial virus A2
Homo sapiens (human)
Respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.28 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
B: Fusion glycoprotein F2
C: Fusion glycoprotein F2
D: 1G12 Fab heavy chain
E: 1G12 Fab light chain
H: 1G12 Fab heavy chain
L: 1G12 Fab light chain
F: 1G12 Fab heavy chain
G: 1G12 Fab light chain
I: Fusion glycoprotein F0,Fibritin
J: Fusion glycoprotein F0,Fibritin
K: Fusion glycoprotein F0,Fibritin


Theoretical massNumber of molelcules
Total (without water)307,23512
Polymers307,23512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.982, 174.605, 226.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fusion glycoprotein F2


Mass: 8173.327 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P03420
#2: Antibody 1G12 Fab heavy chain


Mass: 25313.207 Da / Num. of mol.: 3
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)
#3: Antibody 1G12 Fab light chain


Mass: 23316.137 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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.: 3
Source method: isolated from a genetically manipulated source
Details: Escherichia phage T2 fibritin trimerization domain fused to C-terminal end,Escherichia phage T2 fibritin trimerization domain fused to C-terminal end
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: 4.63 Å3/Da / Density % sol: 73.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium sulfate, 20 % w/v PEG 3350

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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: Mar 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.28→46.95 Å / Num. obs: 36919 / % possible obs: 72.86 % / Redundancy: 7.3 % / CC1/2: 0.94 / Net I/σ(I): 7.2
Reflection shellResolution: 4.28→4.43 Å / Num. unique obs: 1605 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.20.1.4487refinement
SERGUIdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.28→46.95 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 1999 6.87 %
Rwork0.2436 --
obs0.246 29107 72.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.28→46.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20187 0 0 0 20187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d5.0792796
X-RAY DIFFRACTIONf_chiral_restr0.0433267
X-RAY DIFFRACTIONf_plane_restr0.0053540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.28-4.390.3601760.2871025X-RAY DIFFRACTION39
4.39-4.510.2652880.28231196X-RAY DIFFRACTION46
4.51-4.640.3585970.27311328X-RAY DIFFRACTION51
4.64-4.790.31351100.27291479X-RAY DIFFRACTION57
4.79-4.960.31121200.25521631X-RAY DIFFRACTION62
4.96-5.160.32041270.25681726X-RAY DIFFRACTION65
5.16-5.390.33791330.26331794X-RAY DIFFRACTION68
5.39-5.670.28091370.24331864X-RAY DIFFRACTION71
5.67-6.030.29851490.26062022X-RAY DIFFRACTION76
6.03-6.490.30631690.27142296X-RAY DIFFRACTION86
6.49-7.150.27451930.24922619X-RAY DIFFRACTION98
7.15-8.170.26581970.232679X-RAY DIFFRACTION100
8.17-10.280.21761980.19352695X-RAY DIFFRACTION99
10.28-46.950.23972050.2272754X-RAY DIFFRACTION97

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