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- PDB-5tpn: Crystal structure of RSV F in complex with human antibody hRSV90 -

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Basic information

Entry
Database: PDB / ID: 5tpn
TitleCrystal structure of RSV F in complex with human antibody hRSV90
Components
  • Fusion glycoprotein F0,Fibritin
  • hRSV0 light chain
  • hRSV90 heavy chain
KeywordsIMMUNE SYSTEM / fusion protein / respiratory syncytial virus / antibody
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / 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 / membrane / identical protein binding
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fibritin
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Enterobacteria phage Ox2 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.141 Å
AuthorsMousa, J.J. / Crowe, J.E.
CitationJournal: To Be Published
Title: Crystal structure of RSV F in complex with human antibody hRSV90
Authors: Mousa, J.J. / Crowe, J.E.
History
DepositionOct 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F0,Fibritin
H: hRSV90 heavy chain
L: hRSV0 light chain


Theoretical massNumber of molelcules
Total (without water)103,6773
Polymers103,6773
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.250, 148.250, 538.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Fusion glycoprotein F0,Fibritin / Protein F


Mass: 56137.848 Da / Num. of mol.: 1 / Mutation: N67I, S215P, I379V, M447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A, (gene. exp.) Enterobacteria phage Ox2 (virus)
Strain: A2 / Gene: wac / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: Q38650
#2: Antibody hRSV90 heavy chain


Mass: 24236.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody hRSV0 light chain


Mass: 23302.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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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: 5.53 Å3/Da / Density % sol: 77.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG, 400/200 mM MgCl2, 6H2O/100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 3.1→49.289 Å / Num. obs: 30527 / % possible obs: 75.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.10.1_2155-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C6B, 4Q9Q

5c6b

4q9q


Resolution: 3.141→49.289 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 1541 5.05 %
Rwork0.2243 --
obs0.2263 30517 75.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.141→49.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7073 0 0 0 7073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127218
X-RAY DIFFRACTIONf_angle_d1.4529812
X-RAY DIFFRACTIONf_dihedral_angle_d16.3662645
X-RAY DIFFRACTIONf_chiral_restr0.0721140
X-RAY DIFFRACTIONf_plane_restr0.0081244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1407-3.24210.3946110.4042192X-RAY DIFFRACTION6
3.2421-3.3580.3182280.3601630X-RAY DIFFRACTION18
3.358-3.49240.3385650.34221225X-RAY DIFFRACTION36
3.4924-3.65130.30661390.31192399X-RAY DIFFRACTION70
3.6513-3.84370.36651660.30563455X-RAY DIFFRACTION100
3.8437-4.08440.2771840.26173472X-RAY DIFFRACTION100
4.0844-4.39960.28021930.20883434X-RAY DIFFRACTION100
4.3996-4.8420.25421810.17473484X-RAY DIFFRACTION100
4.842-5.54180.21521840.18473507X-RAY DIFFRACTION100
5.5418-6.97890.26972020.22363508X-RAY DIFFRACTION100
6.9789-49.29470.21551880.2053670X-RAY DIFFRACTION99

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