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- PDB-5j3d: Crystal structure of human Fab 14N4 in complex with post-fusion RSV F -

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Basic information

Entry
Database: PDB / ID: 5j3d
TitleCrystal structure of human Fab 14N4 in complex with post-fusion RSV F
Components
  • (Fusion glycoprotein F0) x 2
  • 14N4 heavy chain
  • 14N4 light chain
KeywordsIMMUNE SYSTEM / antibody / virus / complex
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / 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 / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / 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 / 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 / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHomo sapiens (human)
Human respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.077 Å
AuthorsMousa, J.J. / Crowe, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for nonneutralizing antibody competition at antigenic site II of the respiratory syncytial virus fusion protein.
Authors: Mousa, J.J. / Sauer, M.F. / Sevy, A.M. / Finn, J.A. / Bates, J.T. / Alvarado, G. / King, H.G. / Loerinc, L.B. / Fong, R.H. / Doranz, B.J. / Correia, B.E. / Kalyuzhniy, O. / Wen, X. / ...Authors: Mousa, J.J. / Sauer, M.F. / Sevy, A.M. / Finn, J.A. / Bates, J.T. / Alvarado, G. / King, H.G. / Loerinc, L.B. / Fong, R.H. / Doranz, B.J. / Correia, B.E. / Kalyuzhniy, O. / Wen, X. / Jardetzky, T.S. / Schief, W.R. / Ohi, M.D. / Meiler, J. / Crowe, J.E.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14N4 heavy chain
B: 14N4 light chain
C: 14N4 heavy chain
D: 14N4 light chain
E: Fusion glycoprotein F0
F: Fusion glycoprotein F0
G: Fusion glycoprotein F0
H: 14N4 heavy chain
I: Fusion glycoprotein F0
J: Fusion glycoprotein F0
K: Fusion glycoprotein F0
L: 14N4 light chain


Theoretical massNumber of molelcules
Total (without water)299,05012
Polymers299,05012
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)235.130, 235.130, 220.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Antibody 14N4 heavy chain


Mass: 23597.490 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 14N4 light chain


Mass: 24001.520 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Fusion glycoprotein F0 / Protein F


Mass: 8301.455 Da / Num. of mol.: 3 / Fragment: UNP residues 26-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A / Production host: Homo sapiens (human) / References: UniProt: P03420
#4: Protein Fusion glycoprotein F0 / Protein F


Mass: 43782.762 Da / Num. of mol.: 3 / Fragment: UNP residues 147-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A / Production host: Homo sapiens (human) / References: UniProt: P03420

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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: 5.17 Å3/Da / Density % sol: 76.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 2 M ammonium sulfate, 5% 2-propanol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 4.077→49.5 Å / Num. obs: 91490 / % possible obs: 98.1 % / Redundancy: 8.3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.296 / Net I/σ(I): 5.5
Reflection shellResolution: 4.077→4.25 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.191 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.511 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRR

3rrr


Resolution: 4.077→49.5 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2819 3765 4.12 %
Rwork0.2568 --
obs0.2579 91490 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.077→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19902 0 0 0 19902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00920301
X-RAY DIFFRACTIONf_angle_d1.31727585
X-RAY DIFFRACTIONf_dihedral_angle_d15.5897464
X-RAY DIFFRACTIONf_chiral_restr0.0613225
X-RAY DIFFRACTIONf_plane_restr0.0093474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0769-4.12850.35061310.33972557X-RAY DIFFRACTION77
4.1285-4.18280.38631290.32443234X-RAY DIFFRACTION97
4.1828-4.240.35661490.31773244X-RAY DIFFRACTION97
4.24-4.30060.3241070.3093297X-RAY DIFFRACTION98
4.3006-4.36470.30641330.29553310X-RAY DIFFRACTION99
4.3647-4.43290.28051590.28223281X-RAY DIFFRACTION99
4.4329-4.50550.30581360.2873255X-RAY DIFFRACTION98
4.5055-4.58320.28581360.27343340X-RAY DIFFRACTION98
4.5832-4.66640.30421380.26353306X-RAY DIFFRACTION99
4.6664-4.75610.28151450.26793271X-RAY DIFFRACTION99
4.7561-4.85310.28931520.26523264X-RAY DIFFRACTION99
4.8531-4.95860.30531530.27123308X-RAY DIFFRACTION99
4.9586-5.07380.27741100.25493272X-RAY DIFFRACTION98
5.0738-5.20050.26741490.25723332X-RAY DIFFRACTION98
5.2005-5.3410.31221290.25243274X-RAY DIFFRACTION98
5.341-5.4980.23761470.28423252X-RAY DIFFRACTION98
5.498-5.67520.3351430.28033295X-RAY DIFFRACTION99
5.6752-5.87770.29821480.27493317X-RAY DIFFRACTION98
5.8777-6.11260.29971470.27983231X-RAY DIFFRACTION98
6.1126-6.39030.28351430.27633269X-RAY DIFFRACTION98
6.3903-6.72640.321370.28743291X-RAY DIFFRACTION98
6.7264-7.14670.29951450.25843272X-RAY DIFFRACTION98
7.1467-7.69660.27811400.23953267X-RAY DIFFRACTION98
7.6966-8.46770.24671400.21223272X-RAY DIFFRACTION97
8.4677-9.6850.19841320.18433246X-RAY DIFFRACTION98
9.685-12.1720.22931440.18563234X-RAY DIFFRACTION97
12.172-49.50390.28781430.28173234X-RAY DIFFRACTION97

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