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- PDB-6h9y: Unraveling the role of the secretor antigen in human rotavirus at... -

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Basic information

Entry
Database: PDB / ID: 6h9y
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 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 / host cell membrane / viral capsid / symbiont entry into host cell / 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 / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...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 / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
VP4 / Outer capsid protein VP4
Similarity search - Component
Biological speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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 / pdbx_seq_map_depositor_info
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 / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6934
Polymers37,1012
Non-polymers5932
Water9,224512
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9342
Polymers18,5501
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7602
Polymers18,5501
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.988, 54.725, 67.433
Angle α, β, γ (deg.)90.000, 97.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer capsid protein VP4


Mass: 18550.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: G1 and S2 are residuals from tag digestion / Source: (gene. exp.) Human rotavirus A / Gene: VP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K9UWM4, UniProt: Q0PRF2*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 1.92 Å3/Da / Density % sol: 35.95 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 1.5M Li2SO4 0.1M Tris pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97907 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: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.31→66.79 Å / Num. obs: 64030 / % possible obs: 94.9 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.053 / Rrim(I) all: 0.102 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.31-1.382.80.695820.7390.4190.73697.6
4.14-54.723.60.05522130.9930.0320.06499.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H9W

6h9w


Resolution: 1.31→66.79 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.0633 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.065
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3204 5 %RANDOM
Rwork0.1806 ---
obs0.1821 60807 94.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 62.69 Å2 / Biso mean: 12.386 Å2 / Biso min: 5.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å2-0.42 Å2
2---0.29 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.31→66.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 40 512 3162
Biso mean--18.18 24.89 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022771
X-RAY DIFFRACTIONr_bond_other_d00.022369
X-RAY DIFFRACTIONr_angle_refined_deg2.1061.9263787
X-RAY DIFFRACTIONr_angle_other_deg3.81735530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79624.228149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15915428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3531519
X-RAY DIFFRACTIONr_chiral_restr0.1550.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023101
X-RAY DIFFRACTIONr_gen_planes_other0.0320.02605
LS refinement shellResolution: 1.31→1.344 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 246 -
Rwork0.341 4538 -
all-4784 -
obs--95.58 %

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