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- PDB-6oai: Crystal structure of P[6] rotavirus vp8* complexed with LNFPI -

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Basic information

Entry
Database: PDB / ID: 6oai
TitleCrystal structure of P[6] rotavirus vp8* complexed with LNFPI
ComponentsProtease-sensitive outer capsid protein
KeywordsVIRUS / Rotavirus / host receptor interaction
Function / homology
Function and homology information


viral life cycle / viral capsid / peptidase activity / proteolysis
Similarity search - Function
Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / 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
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. / Jiang, X. / Kennedy, M.A.
CitationJournal: Plos Pathog. / Year: 2020
Title: Molecular basis of P[II] major human rotavirus VP8* domain recognition of histo-blood group antigens.
Authors: Xu, S. / Ahmed, L.U. / Stuckert, M.R. / McGinnis, K.R. / Liu, Y. / Tan, M. / Huang, P. / Zhong, W. / Zhao, D. / Jiang, X. / Kennedy, M.A.
History
DepositionMar 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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 / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Protease-sensitive outer capsid protein
B: Protease-sensitive outer capsid protein
C: Protease-sensitive outer capsid protein
D: Protease-sensitive outer capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6285
Polymers73,7744
Non-polymers8541
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint7 kcal/mol
Surface area26410 Å2
2
A: Protease-sensitive outer capsid protein


Theoretical massNumber of molelcules
Total (without water)18,4431
Polymers18,4431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Protease-sensitive outer capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2972
Polymers18,4431
Non-polymers8541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Protease-sensitive outer capsid protein


Theoretical massNumber of molelcules
Total (without water)18,4431
Polymers18,4431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Protease-sensitive outer capsid protein


Theoretical massNumber of molelcules
Total (without water)18,4431
Polymers18,4431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.690, 75.870, 74.927
Angle α, β, γ (deg.)90.000, 91.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protease-sensitive outer capsid protein


Mass: 18443.498 Da / Num. of mol.: 4 / Fragment: VP8* domain, residues 49-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Production host: Escherichia coli (E. coli) / References: UniProt: D2DXN5
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 853.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[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/a4-b1_b3-c1_c3-d1_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]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate, 1.0 M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.9→74.89 Å / Num. obs: 48808 / % possible obs: 97.3 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.087 / Net I/σ(I): 12.4 / Num. measured all: 164606
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-23.20.36370160.8670.240.43896.4
6-74.893.30.02416150.9990.0160.02997.9

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NIW

6niw


Resolution: 1.9→45.95 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.182 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.166
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 2342 4.8 %RANDOM
Rwork0.1947 ---
obs0.1972 46445 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.03 Å2 / Biso mean: 19.793 Å2 / Biso min: 4.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20.95 Å2
2---0.67 Å20 Å2
3---1.88 Å2
Refinement stepCycle: final / Resolution: 1.9→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5188 0 58 148 5394
Biso mean--34.36 18.71 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135394
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174659
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6717363
X-RAY DIFFRACTIONr_angle_other_deg1.3291.58610906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7485629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63524.306288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10415870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1951516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.025920
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021118
LS refinement shellResolution: 1.898→1.948 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 181 -
Rwork0.246 3268 -
all-3449 -
obs--93.65 %

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