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- PDB-3fmg: Structure of rotavirus outer capsid protein VP7 trimer in complex... -

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Basic information

Entry
Database: PDB / ID: 3fmg
TitleStructure of rotavirus outer capsid protein VP7 trimer in complex with a neutralizing Fab
Components
  • Fab of neutralizing antibody 4F8, heavy chain
  • Fab of neutralizing antibody 4F8, light chain
  • Glycoprotein VP7
KeywordsIMMUNE SYSTEM / antibody-antigen complex / calcium dependent trimer / antiparallel beta-sandwich / jelly roll / alpha-beta-alpha sandwich / Rossmann fold / Capsid protein / Endoplasmic reticulum / Glycoprotein / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / viral outer capsid / receptor-mediated virion attachment to host cell / metal ion binding
Similarity search - Function
Rotavirus outer-layer protein VP7, domain 2 / Glycoprotein VP7, domain 1 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich ...Rotavirus outer-layer protein VP7, domain 2 / Glycoprotein VP7, domain 1 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Outer capsid glycoprotein VP7
Similarity search - Component
Biological speciesSimian rotavirus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsAoki, S.T. / Settembre, E.C. / Trask, S.D. / Greenberg, H.B. / Harrison, S.C. / Dormitzer, P.R.
CitationJournal: Science / Year: 2009
Title: Structure of rotavirus outer-layer protein VP7 bound with a neutralizing Fab.
Authors: Aoki, S.T. / Settembre, E.C. / Trask, S.D. / Greenberg, H.B. / Harrison, S.C. / Dormitzer, P.R.
History
DepositionDec 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab of neutralizing antibody 4F8, light chain
H: Fab of neutralizing antibody 4F8, heavy chain
A: Glycoprotein VP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2825
Polymers78,2023
Non-polymers802
Water00
1
L: Fab of neutralizing antibody 4F8, light chain
H: Fab of neutralizing antibody 4F8, heavy chain
A: Glycoprotein VP7
hetero molecules

L: Fab of neutralizing antibody 4F8, light chain
H: Fab of neutralizing antibody 4F8, heavy chain
A: Glycoprotein VP7
hetero molecules

L: Fab of neutralizing antibody 4F8, light chain
H: Fab of neutralizing antibody 4F8, heavy chain
A: Glycoprotein VP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,84515
Polymers234,6059
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Unit cell
Length a, b, c (Å)244.179, 244.179, 244.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Antibody Fab of neutralizing antibody 4F8, light chain


Mass: 23252.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab of neutralizing antibody 4F8, heavy chain


Mass: 23716.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse)
#3: Protein Glycoprotein VP7 / Serotype-specific antigen / Outer capsid glycoprotein


Mass: 31232.234 Da / Num. of mol.: 1 / Fragment: trimer subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus / Strain: RRV / Gene: S9, VP7 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P12476
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Sequence detailsA171T AND N324Y ARE NATURAL VARIANTS.

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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

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM Na citrate, 5% PEG 4K, 200 mM NaCl, 0.1 mM CaCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorDetector: CCD / Date: Oct 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 34017 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 15.4
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.483 / Num. unique all: 3376 / Rsym value: 0.717 / % possible all: 99.2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1dbm

1dbm


Resolution: 3.4→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2377 3167 -
Rwork0.2236 --
all-31889 -
obs-28722 82.8 %
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5164 0 2 0 5166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONdihedral angles (degrees)27
X-RAY DIFFRACTIONimproper angles (degrees)1.58
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.354 492 -
Rwork0.347 --
obs-4332 85.2 %

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