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- PDB-6h9w: Unraveling the role of the secretor antigen in human rotavirus at... -

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Basic information

Entry
Database: PDB / ID: 6h9w
TitleUnraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / histo-blood group antigen rotavirus
Function / homology
Function and homology information


host cell endoplasmic reticulum / host cell membrane / viral capsid / symbiont entry into host cell / virion attachment to host cell / membrane
Similarity search - Function
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
CITRIC ACID / ISOPROPYL ALCOHOL / Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsCiges-Tomas, J.R. / Gozalbo-Rovira, R. / Vila-Vicent, S. / Buesa, J. / Santiso-Bellon, C. / Monedero, V. / Yebra, M.J. / Rodriguez-Diaz, J. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
CitationJournal: Plos Pathog. / Year: 2019
Title: Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens.
Authors: Gozalbo-Rovira, R. / Ciges-Tomas, J.R. / Vila-Vicent, S. / Buesa, J. / Santiso-Bellon, C. / Monedero, V. / Yebra, M.J. / Marina, A. / Rodriguez-Diaz, J.
History
DepositionAug 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2478
Polymers18,5501
Non-polymers6977
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-27 kcal/mol
Surface area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.148, 76.148, 70.084
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-205-

CIT

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Components

#1: Protein Outer capsid protein VP4


Mass: 18550.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: G1 and S2 are residuals from tag digestion / Source: (gene. exp.) Rotavirus A / Gene: VP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S0VKY7
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 1.2M (NH 4 ) 2 SO 4 3% iso-propanol and 0.1M sodium citrate pH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.35→65.95 Å / Num. obs: 52302 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 15.9
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7527 / CC1/2: 0.932 / Rpim(I) all: 0.266 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless5.8.0158data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I2S

2i2s


Resolution: 1.35→65.95 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.201 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 2612 5 %RANDOM
Rwork0.2058 ---
obs0.2069 49656 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.2 Å2 / Biso mean: 27.175 Å2 / Biso min: 14.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å2-0 Å2
3----2.39 Å2
Refinement stepCycle: final / Resolution: 1.35→65.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 41 211 1544
Biso mean--38.74 39.09 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.021385
X-RAY DIFFRACTIONr_bond_other_d0.0030.021164
X-RAY DIFFRACTIONr_angle_refined_deg2.7031.9351894
X-RAY DIFFRACTIONr_angle_other_deg1.2532711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93924.47476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84815209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.539159
X-RAY DIFFRACTIONr_chiral_restr0.1640.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021548
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02297
LS refinement shellResolution: 1.347→1.382 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 193 -
Rwork0.34 3608 -
all-3801 -
obs--99.14 %

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