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- PDB-5vki: Crystal structure of P[19] rotavirus VP8* complexed with mucin core 2 -

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Basic information

Entry
Database: PDB / ID: 5vki
TitleCrystal structure of P[19] rotavirus VP8* complexed with mucin core 2
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / complex / P[19]VP8* / mucin core 2
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / 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-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
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
THREONINE / Outer capsid protein VP4
Similarity search - Component
Biological speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXu, S. / Liu, Y. / Woodruff, A. / Zhong, W. / Jiang, X. / Kennedy, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R56AI11483-01A1 United States
CitationJournal: PLoS Pathog. / Year: 2017
Title: Structural basis of glycan specificity of P[19] VP8*: Implications for rotavirus zoonosis and evolution.
Authors: Liu, Y. / Xu, S. / Woodruff, A.L. / Xia, M. / Tan, M. / Kennedy, M.A. / Jiang, X.
History
DepositionApr 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)38,12010
Polymers36,3322
Non-polymers1,7888
Water3,639202
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0605
Polymers18,1661
Non-polymers8944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0605
Polymers18,1661
Non-polymers8944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.861, 115.861, 101.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 64 - 223 / Label seq-ID: 1 - 160

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.000217, 1, -0.000318), (1, -0.000217, 0.000254), (0.000254, -0.000318, -1)-9.0E-5, 0.00383, -18.764669

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Outer capsid protein VP4 / VP8*


Mass: 18166.168 Da / Num. of mol.: 2 / Fragment: UNP residues 64-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Gene: VP4 / Production host: Escherichia coli (E. coli) / References: UniProt: A7YCM0
#2: Polysaccharide beta-D-galactopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy- ...beta-D-galactopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3[DGlcpNAcb1-6]DGalpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}[(6+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 208 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-THR / THREONINE / Threonine


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 4.7 Å3/Da / Density % sol: 73.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 1.0 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225HE / Detector: CCD / Date: Mar 22, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.9→32.55 Å / Num. all: 52865 / Num. obs: 52865 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.071 / Rrim(I) all: 0.195 / Rsym value: 0.182 / Net I/σ(I): 7.2 / Num. measured all: 401407
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-27.50.7945793277360.8310.0230.0620.0572.4100
6.01-32.557.30.0571229916940.9970.0280.0760.0716.898.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5GJ6

5gj6


Resolution: 1.9→32.55 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.335 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 2640 5 %RANDOM
Rwork0.2208 ---
obs0.2218 50115 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.63 Å2 / Biso mean: 26.892 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å2-0 Å20 Å2
2---1.46 Å2-0 Å2
3---2.93 Å2
Refinement stepCycle: final / Resolution: 1.9→32.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 116 202 2880
Biso mean--47.07 34.2 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192740
X-RAY DIFFRACTIONr_bond_other_d0.0010.022386
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.933744
X-RAY DIFFRACTIONr_angle_other_deg0.7652.9535582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4485318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16624.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79815428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6591510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02532
Refine LS restraints NCSNumber: 1281 / Type: TIGHT THERMAL / Rms dev position: 0.97 Å / Weight position: 0.5
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.523 185 -
Rwork0.507 3657 -
all-3842 -
obs--98.41 %

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