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- PDB-6ha0: Unraveling the role of the secretor antigen in human rotavirus at... -

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Basic information

Entry
Database: PDB / ID: 6ha0
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
H type 1 antigen, beta anomer / Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)37,6303
Polymers37,1012
Non-polymers5291
Water3,225179
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0802
Polymers18,5501
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,5501
Polymers18,5501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.739, 54.641, 67.944
Angle α, β, γ (deg.)90.000, 97.730, 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: First two residues (GS) are coming from the tag / Source: (gene. exp.) Rotavirus A / Gene: VP4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S0VKY7
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose / H type 1 antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: H type 1 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 35.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 25%PEG 6000 0.1M Na-HEPES pH7.5 0.1M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97928 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: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.85→67.33 Å / Num. obs: 23811 / % possible obs: 99.2 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.053 / Rrim(I) all: 0.103 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.950.69934470.7460.4310.82498.9
5.86-54.640.0358030.9960.0210.04199.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H9W

6h9w


Resolution: 1.85→67.33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.053 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.155
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 1162 4.9 %RANDOM
Rwork0.1761 ---
obs0.1788 22633 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.76 Å2 / Biso mean: 25.359 Å2 / Biso min: 13.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å2-0 Å2-1.74 Å2
2---2.53 Å20 Å2
3---1.36 Å2
Refinement stepCycle: final / Resolution: 1.85→67.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 36 179 2819
Biso mean--34.13 32.88 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022712
X-RAY DIFFRACTIONr_bond_other_d0.0020.022299
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9263696
X-RAY DIFFRACTIONr_angle_other_deg1.00135359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8415320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28424.345145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85315412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6061517
X-RAY DIFFRACTIONr_chiral_restr0.1060.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
LS refinement shellResolution: 1.854→1.902 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 77 -
Rwork0.344 1652 -
all-1729 -
obs--98.74 %

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