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- PDB-5u68: Structural basis for antibody cross-neutralization of respiratory... -

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Basic information

Entry
Database: PDB / ID: 5u68
TitleStructural basis for antibody cross-neutralization of respiratory syncytial virus and human metapneumovirus
Components
  • Chimera protein of Fusion glycoprotein F0 and Envelope glycoprotein
  • MPE8
KeywordsVIRAL PROTEIN/Immune System / RSVF prefusion / MPE8 / cross-reactive antibody neutralization / Trimer / VIRAL PROTEIN-Immune System complex
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
Envelope glycoprotein / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Human immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.083 Å
AuthorsWen, X. / Jardetzky, T.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-61050 United States
CitationJournal: Nat Microbiol / Year: 2017
Title: Structural basis for antibody cross-neutralization of respiratory syncytial virus and human metapneumovirus.
Authors: Wen, X. / Mousa, J.J. / Bates, J.T. / Lamb, R.A. / Crowe, J.E. / Jardetzky, T.S.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Source and taxonomy
Revision 1.2Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of Fusion glycoprotein F0 and Envelope glycoprotein
B: Chimera protein of Fusion glycoprotein F0 and Envelope glycoprotein
C: Chimera protein of Fusion glycoprotein F0 and Envelope glycoprotein
E: MPE8
F: MPE8
G: MPE8


Theoretical massNumber of molelcules
Total (without water)279,4116
Polymers279,4116
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)155.540, 155.540, 275.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Chimera protein of Fusion glycoprotein F0 and Envelope glycoprotein / / Protein F


Mass: 62452.488 Da / Num. of mol.: 3
Fragment: UNP P03420 residues 1-513,UNP M1E1E4 residues 1-28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2), (gene. exp.) Human immunodeficiency virus 1
Strain: A2 / Plasmid: pTT5 / Cell line (production host): 293-6E / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: M1E1E4
#2: Antibody MPE8


Mass: 30684.664 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: single chain antibody (scFv) / Source: (gene. exp.) Homo sapiens (human) / Production host: 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: 3.45 Å3/Da / Density % sol: 64.36 % / Description: rod-shaped
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Potassium Nitrate, 0.1M Citrate Phosphate pH 4.2, 1 % Tacsimate pH 7.0, 14 (w/v) % PEG 6000
PH range: 7.0-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 13, 2015 / Details: Fibre Optic Taper (FOT)
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.1→48.191 Å / Num. obs: 71891 / % possible obs: 99.98 % / Redundancy: 11.2 % / Net I/σ(I): 11.96

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JHW, 3H42

4jhw

3h42


Resolution: 3.083→48.191 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 2686 5.01 %Random
Rwork0.1842 ---
obs0.187 53648 74.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.083→48.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15642 0 0 0 15642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02115933
X-RAY DIFFRACTIONf_angle_d1.89321561
X-RAY DIFFRACTIONf_dihedral_angle_d17.2565778
X-RAY DIFFRACTIONf_chiral_restr0.0812526
X-RAY DIFFRACTIONf_plane_restr0.012733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0832-3.13930.2965100.505128X-RAY DIFFRACTION4
3.1393-3.19970.4795200.3663343X-RAY DIFFRACTION10
3.1997-3.2650.571330.3435574X-RAY DIFFRACTION16
3.265-3.33590.453430.3198873X-RAY DIFFRACTION25
3.3359-3.41350.3379690.29931249X-RAY DIFFRACTION35
3.4135-3.49890.3162910.28431724X-RAY DIFFRACTION49
3.4989-3.59340.31711350.25012654X-RAY DIFFRACTION74
3.5934-3.69910.31831900.23383594X-RAY DIFFRACTION100
3.6991-3.81850.31371860.22523549X-RAY DIFFRACTION100
3.8185-3.95490.27841890.20443578X-RAY DIFFRACTION100
3.9549-4.11320.24671880.18183569X-RAY DIFFRACTION100
4.1132-4.30020.20111870.15543565X-RAY DIFFRACTION100
4.3002-4.52680.19781900.13753600X-RAY DIFFRACTION100
4.5268-4.81020.16851900.133598X-RAY DIFFRACTION100
4.8102-5.18120.20681900.13723607X-RAY DIFFRACTION100
5.1812-5.70180.20911890.14843613X-RAY DIFFRACTION100
5.7018-6.52520.22341920.1643652X-RAY DIFFRACTION100
6.5252-8.21440.22471940.18853680X-RAY DIFFRACTION100
8.2144-48.19660.22862000.20773812X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -135.4741 Å / Origin y: 162.3403 Å / Origin z: 288.1867 Å
111213212223313233
T0.4693 Å2-0.2245 Å20.0112 Å2-0.2526 Å20.0752 Å2--0.4118 Å2
L0.7689 °20.0393 °20.5156 °2-0.6538 °20.2363 °2--1.0335 °2
S0.0759 Å °-0.2541 Å °-0.1502 Å °0.1485 Å °0.0141 Å °-0.0789 Å °0.1678 Å °-0.0763 Å °-0.0386 Å °
Refinement TLS groupSelection details: all

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