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- PDB-5vx5: VP8* of a G2P[4] Human Rotavirus in complex with LNFP1 -

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Basic information

Entry
Database: PDB / ID: 5vx5
TitleVP8* of a G2P[4] Human Rotavirus in complex with LNFP1
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / Glycan / HBGA / rotavirus
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral capsid / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane
Similarity search - Function
Rotavirus VP4, membrane interaction domain superfamily / 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 speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.285 Å
AuthorsHu, L. / Venkataram Prasad, B.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36040 United States
Robert A. Welch FoundationQ1279 United States
CitationJournal: Nat Commun / Year: 2018
Title: Glycan recognition in globally dominant human rotaviruses.
Authors: Hu, L. / Sankaran, B. / Laucirica, D.R. / Patil, K. / Salmen, W. / Ferreon, A.C.M. / Tsoi, P.S. / Lasanajak, Y. / Smith, D.F. / Ramani, S. / Atmar, R.L. / Estes, M.K. / Ferreon, J.C. / Prasad, B.V.V.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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_atom_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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3522
Polymers18,4981
Non-polymers8541
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint22 kcal/mol
Surface area7730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.790, 50.240, 110.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer capsid protein VP4 / Indian G2P[4] rotavirus VP8*


Mass: 18498.297 Da / Num. of mol.: 1 / Fragment: UNP residues 54-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2VE61
#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.: 399 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate, 0.1 M Tris, pH 8.5, 30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2015
RadiationMonochromator: Single crystal, cylindrically bent Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.285→28.04 Å / Num. obs: 89379 / % possible obs: 93.41 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.022 / Net I/σ(I): 19.58
Reflection shellHighest resolution: 1.285 Å / Rmerge(I) obs: 0.269 / CC1/2: 0.963 / Rpim(I) all: 0.102

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLM7.0.9data reduction
SCALA3.3.21data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AEN

2aen


Resolution: 1.285→28.04 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 0.99 / Phase error: 15.09
RfactorNum. reflection% reflection
Rfree0.1672 2334 5.1 %
Rwork0.1529 --
obs0.1537 45769 91.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.285→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1302 0 58 399 1759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061472
X-RAY DIFFRACTIONf_angle_d1.1042018
X-RAY DIFFRACTIONf_dihedral_angle_d12.366644
X-RAY DIFFRACTIONf_chiral_restr0.042227
X-RAY DIFFRACTIONf_plane_restr0.005258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.285-1.29960.20181250.20542382X-RAY DIFFRACTION80
1.2996-1.31490.22731610.19212455X-RAY DIFFRACTION86
1.3149-1.33090.19051150.19032488X-RAY DIFFRACTION86
1.3309-1.34780.18381370.17652523X-RAY DIFFRACTION84
1.3478-1.36550.21191300.17942538X-RAY DIFFRACTION87
1.3655-1.38420.20871490.17572488X-RAY DIFFRACTION86
1.3842-1.4040.23261250.17682518X-RAY DIFFRACTION85
1.404-1.4250.17231300.16242532X-RAY DIFFRACTION87
1.425-1.44720.15361320.16412551X-RAY DIFFRACTION86
1.4472-1.4710.14771170.15692576X-RAY DIFFRACTION86
1.471-1.49630.15091310.15112592X-RAY DIFFRACTION90
1.4963-1.52350.13311450.1512623X-RAY DIFFRACTION88
1.5235-1.55280.17611490.14772646X-RAY DIFFRACTION91
1.5528-1.58450.18071570.14532680X-RAY DIFFRACTION91
1.5845-1.6190.15951220.15472717X-RAY DIFFRACTION91
1.619-1.65660.17791320.14942734X-RAY DIFFRACTION93
1.6566-1.69810.17681400.14782770X-RAY DIFFRACTION94
1.6981-1.7440.20121660.15422781X-RAY DIFFRACTION95
1.744-1.79530.16441680.14972803X-RAY DIFFRACTION95
1.7953-1.85320.13711680.15282799X-RAY DIFFRACTION96
1.8532-1.91940.14051410.15642842X-RAY DIFFRACTION97
1.9194-1.99630.18591390.14732913X-RAY DIFFRACTION98
1.9963-2.08710.16341810.14732850X-RAY DIFFRACTION98
2.0871-2.19710.15821700.15022833X-RAY DIFFRACTION98
2.1971-2.33470.17421350.15252927X-RAY DIFFRACTION99
2.3347-2.51490.17711520.15522895X-RAY DIFFRACTION98
2.5149-2.76780.14931600.16822907X-RAY DIFFRACTION99
2.7678-3.16790.15841720.14522792X-RAY DIFFRACTION96
3.1679-3.98970.16081360.13962927X-RAY DIFFRACTION99
3.9897-29.76910.16431670.13912895X-RAY DIFFRACTION98

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