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- PDB-7jhz: Crystal structure of the carbohydrate-binding domain VP8* of huma... -

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Basic information

Entry
Database: PDB / ID: 7jhz
TitleCrystal structure of the carbohydrate-binding domain VP8* of human P[8] rotavirus strain BM13851 in complex with LNDFH I
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / Rotavirus / host receptor interaction
Function / homologyHaemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / viral capsid / Concanavalin A-like lectin/glucanase domain superfamily / symbiont entry into host cell / virion attachment to host cell / Outer capsid protein VP4
Function and homology information
Biological speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsXu, S. / Stuckert, M.R. / McGinnis, K.R. / Jiang, X. / 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
DepositionJul 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Outer capsid protein VP4
B: Outer capsid protein VP4
C: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2287
Polymers55,2073
Non-polymers2,0224
Water1629
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2402
Polymers18,4021
Non-polymers8381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4942
Polymers18,4021
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4943
Polymers18,4021
Non-polymers1,0922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.192, 63.390, 72.260
Angle α, β, γ (deg.)90.000, 91.150, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Outer capsid protein VP4


Mass: 18402.191 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Gene: VP8 / Production host: Escherichia coli (E. coli) / References: UniProt: M4VPJ0
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 999.912 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-2-4-4/a4-b1_b3-c1_c3-d1_c4-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}[(4+1)][a-L-Fucp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 837.771 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-3-3/a3-b1_b3-c1_b4-e1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}[(4+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.33 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 2% v/v Polyethylene glycol 400,2.0 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: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.68→56.08 Å / Num. obs: 13841 / % possible obs: 95.9 % / Redundancy: 5.1 % / CC1/2: 0.977 / Rmerge(I) obs: 0.183 / Net I/σ(I): 7.1 / Num. measured all: 70641 / Scaling rejects: 164
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.68-2.820.6641072920430.7643.597.6
8.46-56.080.12224984750.97911.896.8

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Processing

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

6vkx


Resolution: 2.68→44.78 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.849 / SU B: 12.946 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.263 608 4.4 %RANDOM
Rwork0.2112 ---
obs0.2135 13225 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.21 Å2 / Biso mean: 23.561 Å2 / Biso min: 5.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0.92 Å2
2---0.25 Å2-0 Å2
3---1.49 Å2
Refinement stepCycle: final / Resolution: 2.68→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 0 133 9 3798
Biso mean--35.48 15.06 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133896
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183416
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.7015326
X-RAY DIFFRACTIONr_angle_other_deg1.3441.6417854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9185443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87622.618233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26315560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4431525
X-RAY DIFFRACTIONr_chiral_restr0.080.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
LS refinement shellResolution: 2.68→2.745 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.265 47 -
Rwork0.229 984 -
obs--97.54 %

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