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- PDB-1slq: Crystal structure of the trimeric state of the rhesus rotavirus V... -

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Basic information

Entry
Database: PDB / ID: 1slq
TitleCrystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT
ComponentsVP4
KeywordsVIRAL PROTEIN / beta sandwich / greek key / alpha helical triple coiled-coil / membrane penetration protein / non-enveloped virus / spike protein
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Concanavalin A-like lectin/glucanase domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Outer capsid protein VP4 / Outer capsid protein VP4
Similarity search - Component
Biological speciesRhesus rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsDormitzer, P.R. / Nason, E.B. / Prasad, B.V.V. / Harrison, S.C.
Citation
Journal: Nature / Year: 2004
Title: Structural rearrangements in the membrane penetration protein of a non-enveloped virus.
Authors: Dormitzer, P.R. / Nason, E.B. / Prasad, B.V. / Harrison, S.C.
#1: Journal: J.Virol. / Year: 2001
Title: Proteolysis of monomeric recombinant rotavirus VP4 yields an oligomeric VP5* core
Authors: Dormitzer, P.R. / Greenberg, H.B. / Harrison, S.C.
#2: Journal: Embo J. / Year: 2002
Title: The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding site
Authors: Dormitzer, P.R. / Sun, Z.-Y.J. / Wagner, G. / Harrison, S.C.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning
Authors: Padilla, J.E. / Yeates, T.O.
History
DepositionMar 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: VP4
B: VP4
C: VP4
D: VP4
E: VP4
F: VP4


Theoretical massNumber of molelcules
Total (without water)187,8486
Polymers187,8486
Non-polymers00
Water0
1
A: VP4
B: VP4
C: VP4


Theoretical massNumber of molelcules
Total (without water)93,9243
Polymers93,9243
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-56 kcal/mol
Surface area33840 Å2
MethodPISA
2
D: VP4
E: VP4
F: VP4


Theoretical massNumber of molelcules
Total (without water)93,9243
Polymers93,9243
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12460 Å2
ΔGint-57 kcal/mol
Surface area33000 Å2
MethodPISA
3
D: VP4
E: VP4
F: VP4

D: VP4
E: VP4
F: VP4


Theoretical massNumber of molelcules
Total (without water)187,8486
Polymers187,8486
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Buried area26600 Å2
ΔGint-128 kcal/mol
Surface area64320 Å2
MethodPISA
4
A: VP4
B: VP4
C: VP4

A: VP4
B: VP4
C: VP4


Theoretical massNumber of molelcules
Total (without water)187,8486
Polymers187,8486
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area25460 Å2
ΔGint-126 kcal/mol
Surface area66310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)244.843, 244.843, 104.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
DetailsThe biological unit is a homotrimer. Each asymmetric unit in space group P4(2)22 contains 2 trimers.

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Components

#1: Protein
VP4


Mass: 31307.945 Da / Num. of mol.: 6
Fragment: Trimeric conformation of the membrane interaction domain, VP5CT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhesus rotavirus / Species: Rotavirus A / Gene: gene segment 4 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q91HI9, UniProt: P12473*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.56 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: ammonium sulfate, MPD, Pipes, Tris, EDTA, sodium azide, benzamidine, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
220 mMTris1drop
31 mMEDTA1drop
40.02 %sodium azide1drop
50.1 mMbenzamidine1drop
66 %ethanol1reservoir
750 mMTris1reservoir
81 mMdithiothreitol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F110.916
SYNCHROTRONCHESS F120.916
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDAug 16, 2002mirrors
ADSC QUANTUM 42CCDFeb 21, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Horizontally bent Si(111)SINGLE WAVELENGTHMx-ray1
2Horizontally bent Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. all: 51973 / Num. obs: 51973 / % possible obs: 99.8 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 23.6
Reflection shellResolution: 3.2→3.27 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 8.8 / Num. unique all: 3446 / Rsym value: 0.12 / % possible all: 99.8
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.8 % / Num. unique obs: 3446 / Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3.2→20 Å / Isotropic thermal model: isotropic by group / Cross valid method: THROUGHOUT / σ(F): 0.01 / Stereochemistry target values: Engh & Huber
Details: An initial model was built to maps calculated with MAD experimental data. The MAD data were collected from crystals of selenomethionine-substituted VP5CT that formed using ethanol as a ...Details: An initial model was built to maps calculated with MAD experimental data. The MAD data were collected from crystals of selenomethionine-substituted VP5CT that formed using ethanol as a precipitant. Refinement proceeded with starting phases from this model and amplitudes from higher resolution data collected from native VP5CT crystals that formed using ammonium sulfate with MPD as a precipitant. All stages of model building and refinement took advantage of 6-fold non-crystallographic symmetry. The resolution of the model is limited by perfect hemihedral twinning, which becomes significant at higher resolutions.
RfactorNum. reflection% reflectionSelection details
Rfree0.338 2599 -Random
Rwork0.308 ---
all0.31 51973 --
obs0.31 51973 99.8 %-
Displacement parametersBiso mean: 91.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.62 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12772 0 0 0 12772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0107
X-RAY DIFFRACTIONc_angle_deg1.591
X-RAY DIFFRACTIONc_dihedral_angle_d24.93
X-RAY DIFFRACTIONc_improper_angle_d0.906
LS refinement shellResolution: 3.2→3.27 Å
RfactorNum. reflection% reflection
Rfree0.488 151 -
Rwork0.443 --
obs-3335 99.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 20 Å / σ(F): 0.01 / Rfactor obs: 0.308
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.93
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.906
LS refinement shell
*PLUS
Rfactor Rfree: 0.488 / Rfactor Rwork: 0.443

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