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- PDB-1kqr: Crystal Structure of the Rhesus Rotavirus VP4 Sialic Acid Binding... -

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Basic information

Entry
Database: PDB / ID: 1kqr
TitleCrystal Structure of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain in Complex with 2-O-methyl-alpha-D-N-acetyl neuraminic acid
ComponentsVP4
KeywordsVIRAL PROTEIN / rotavirus / VP4 / VP8* / spike protein / outer capsid / sialic acid / hemagglutinin / cell attachment / neutralization antigen / lectin / galectin fold
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / permeabilization of host organelle membrane involved in viral entry into host cell / host cytoskeleton / viral outer capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
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 / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...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 / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid / Outer capsid protein VP4
Similarity search - Component
Biological speciesRhesus rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.4 Å
AuthorsDormitzer, P.R. / Sun, Z.-Y.J. / Wagner, G. / Harrison, S.C.
Citation
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.
#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.
History
DepositionJan 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_remark / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_remark.text / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 12The 8 to 16 residue amino terminal linker and residues E62 to V64 of VP4 are disordered and are not ...The 8 to 16 residue amino terminal linker and residues E62 to V64 of VP4 are disordered and are not included in the model.
Remark 13Alternate conformations are modeled for residues Q70, M82, I106, S118, T124, Q125, I141, V143, ...Alternate conformations are modeled for residues Q70, M82, I106, S118, T124, Q125, I141, V143, S151, Y155, G156, P157, Q159, K163, V167, N171, N178, E180, K187, E212, S214, and N222.
Remark 14The G156-P157 peptide bond has alternate cis and trans conformations.
Remark 15The model contains two apparent close contacts: the N222 side chain with HOH 2187 and the G156 ...The model contains two apparent close contacts: the N222 side chain with HOH 2187 and the G156 carbonyl with HOH 2190. In each case, the residue has alternate conformations, and the water molecule has partial occupancy, so that clashes are avoided.
Remark 16The electron density for the K187 side chain is ambiguous beyond CB. A well-defined volume of high ...The electron density for the K187 side chain is ambiguous beyond CB. A well-defined volume of high electron density near K187 is modeled with NZ of K187 conformation B. The low B-factor of this atom (2.63) indicates that, in another conformation, this density is occupied by another atom, possibly an ion, which has not been modeled.
Remark 700sheet determination method: author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7324
Polymers20,2201
Non-polymers5113
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.027, 48.027, 130.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2167-

HOH

21A-2188-

HOH

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Components

#1: Protein VP4


Mass: 20220.279 Da / Num. of mol.: 1 / Fragment: sialic acid binding domain (residues 62-224)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhesus rotavirus / Species: Rotavirus A / Gene: segment 4 / Plasmid: pGex-VP8(62-224) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P12473
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-MNA / 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid / 2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID


Type: D-saccharide / Mass: 323.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21NO9
IdentifierTypeProgram
2-O-methyl-5-N-acetyl-a-D-neuraminic acidIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 1.84 Å3/Da / Density % sol: 25.2 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, PEG 400, NaCl, NaPO4, Pipes, Tris, 2-O-methyl-alpha-D-N-acetyl neuraminic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
117.6 mg/mlprotein1drop
252 mMsialoside1drop
35.6 mMTris-HCl1droppH8.0
414 mMsodium phosphate1droppH7.0
535 mM1dropNaCl
60.3 mMEDTA1drop
70.02 %sodium azide1drop
80.1 mMbenzamidine1drop
91.60-1.75 Mammonium sulfate1reservoir
102.3-2.5 %PEG4001reservoir
11100 mMPIPES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2001 / Details: mirror
RadiationMonochromator: bent G3(III) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 31002 / Num. obs: 31002 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.25 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.4
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 5.71 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 5.51 / Num. unique all: 1993 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 98.3 % / Num. unique obs: 1993

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SIR / Resolution: 1.4→25 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1530 5 %Random
Rwork0.169 ---
all-30898 --
obs-30898 99.5 %-
Displacement parametersBiso mean: 14.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 33 190 1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.86
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_mcbond_it1.2941.5
X-RAY DIFFRACTIONc_mcangle_it1.8522
X-RAY DIFFRACTIONc_scbond_it2.5212
X-RAY DIFFRACTIONc_scangle_it3.2922.5
LS refinement shellResolution: 1.4→1.45 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.22 142 5 %
Rwork0.204 2895 -
obs-3037 99.5 %
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0149
X-RAY DIFFRACTIONc_angle_deg1.858
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.25
LS refinement shell
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.204

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