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- PDB-7ki5: Crystal structure of P[6] rotavirus vp8* in complex with LNT -

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Basic information

Entry
Database: PDB / ID: 7ki5
TitleCrystal structure of P[6] rotavirus vp8* in complex with LNT
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Rotavirus / host receptor interaction / VIRUS
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral capsid / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane
Similarity search - Function
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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Outer capsid protein VP4
Similarity search - Component
Biological speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsXu, S. / Kennedy, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis of P[II] rotavirus evolution and host ranges under selection of histo-blood group antigens.
Authors: Xu, S. / McGinnis, K.R. / Liu, Y. / Huang, P. / Tan, M. / Stuckert, M.R. / Burnside, R.E. / Jacob, E.G. / Ni, S. / Jiang, X. / Kennedy, M.A.
History
DepositionOct 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2138
Polymers74,1714
Non-polymers1,0424
Water5,062281
1
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6932
Polymers18,5431
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2502
Polymers18,5431
Non-polymers7081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6352
Polymers18,5431
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6352
Polymers18,5431
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.681, 75.354, 74.411
Angle α, β, γ (deg.)90.000, 91.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Capsid protein


Mass: 18542.631 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Gene: VP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91E88
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3-2/a4-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2 M Potassium sodium tartrate tetrahydrate,0.1 M Sodium citrate tribasic dihydrate pH 5.6,2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97932 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.52→74.38 Å / Num. obs: 92741 / % possible obs: 96.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Net I/σ(I): 12.4 / Num. measured all: 317719 / Scaling rejects: 276
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.52-1.63.40.6145238133350.8040.3870.7252.694.9
4.8-74.383.30.031994430230.9980.020.03727.996.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UT9

6ut9


Resolution: 1.52→74.38 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.55 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 4797 5.2 %RANDOM
Rwork0.1741 ---
obs0.1753 87918 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74 Å2 / Biso mean: 19.943 Å2 / Biso min: 10.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20.23 Å2
2--0.88 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.52→74.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5172 0 58 281 5511
Biso mean--50.12 29.11 -
Num. residues----631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135388
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184851
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.6627343
X-RAY DIFFRACTIONr_angle_other_deg1.2831.58311197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1235635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93624.306288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77215870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9121516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026089
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021295
LS refinement shellResolution: 1.52→1.556 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.329 357 -
Rwork0.282 6319 -
obs--93.46 %

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