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- PDB-4ds0: Cell attachment protein VP8* of a human rotavirus specifically in... -

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Basic information

Entry
Database: PDB / ID: 4ds0
TitleCell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / OTAVIRUS / CELL ATTACHMENT FACTOR / HISTO BLOOD GROUP ANTIGEN / GALECTIN-FOLD
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
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
Blood group A H type 2 antigen, beta anomer / Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus sp.
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsHu, L. / Crawford, S.E. / Czako, R. / Cortes-Penfield, N.W. / Smith, D.F. / Le Pendu, J. / Estes, M.K. / Prasad, B.V.V.
CitationJournal: Nature / Year: 2012
Title: Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen.
Authors: Hu, L. / Crawford, S.E. / Czako, R. / Cortes-Penfield, N.W. / Smith, D.F. / Le Pendu, J. / Estes, M.K. / Prasad, B.V.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 5, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 2.2Sep 13, 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: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3002
Polymers18,5681
Non-polymers7331
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.750, 35.540, 44.060
Angle α, β, γ (deg.)90.00, 94.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer capsid protein VP4 / Rotavirus cell attachment protein VP8*


Mass: 18567.623 Da / Num. of mol.: 1 / Fragment: UNP residues 64-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus sp. / Gene: VP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86169
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Blood group A H type 2 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b2-c1_b3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 1.84 Å3/Da / Density % sol: 33.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% PEG 1500 Sodium acetate trihydrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.56→27.6 Å / Num. all: 19647 / Num. obs: 19647 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.56→1.64 Å / % possible all: 86.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.4_162) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQR

1kqr


Resolution: 1.56→27.6 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 17.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 939 5.16 %Random
Rwork0.1561 ---
all0.1577 18211 --
obs0.1577 18211 92.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.669 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4105 Å20 Å2-0.5005 Å2
2--2.38 Å2-0 Å2
3----0.9696 Å2
Refinement stepCycle: LAST / Resolution: 1.56→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1307 0 50 273 1630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061392
X-RAY DIFFRACTIONf_angle_d1.0741908
X-RAY DIFFRACTIONf_dihedral_angle_d30.201544
X-RAY DIFFRACTIONf_chiral_restr0.068223
X-RAY DIFFRACTIONf_plane_restr0.004237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.6370.20941140.16922298X-RAY DIFFRACTION87
1.637-1.73950.23251110.1552368X-RAY DIFFRACTION90
1.7395-1.87380.20841240.15582431X-RAY DIFFRACTION91
1.8738-2.06230.16891580.14482438X-RAY DIFFRACTION93
2.0623-2.36060.17731290.14332517X-RAY DIFFRACTION94
2.3606-2.97360.19961520.15142552X-RAY DIFFRACTION96
2.9736-27.62760.15561510.13222668X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0549-0.49540.32280.2421-0.14970.2813-0.0464-0.02120.1076-0.0054-0.0326-0.0017-0.0567-0.03270.06870.0684-0.0115-0.00750.04580.00590.06887.742412.95146.6126
20.28810.14830.15370.1726-0.16270.66340.0708-0.05880.06760.0486-0.0241-0.00260.0282-0.0225-0.04010.0562-0.02080.01310.054-0.01710.051118.55087.200118.8323
30.1655-0.08040.18950.1622-0.00770.725-0.00480.0471-0.0066-0.0354-0.01460.03680.0704-0.04790.01710.0451-0.0091-0.00030.04220.00230.053210.52433.9047.2653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 62:96)
2X-RAY DIFFRACTION2chain 'A' and (resseq 97:145)
3X-RAY DIFFRACTION3chain 'A' and (resseq 146:224)

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