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

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Basic information

Entry
Database: PDB / ID: 4drv
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 / permeabilization of host organelle membrane involved in viral entry into host cell / host cytoskeleton / viral outer capsid / 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 / 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 ...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 / 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 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.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 2.1Sep 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)19,0972
Polymers18,5681
Non-polymers5291
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.720, 35.220, 43.990
Angle α, β, γ (deg.)90.00, 95.45, 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)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 1.82 Å3/Da / Density % sol: 32.26 %
Crystal growTemperature: 293 K / 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

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.56→27.44 Å / Num. obs: 19362 / % possible obs: 99.4 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.56→1.64 Å / % possible all: 96.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQR

1kqr


Resolution: 1.56→27.44 Å / SU ML: 0.21 / σ(F): 1.45 / Phase error: 15.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.178 989 5.11 %
Rwork0.15 --
obs0.152 19351 99.7 %
all-19351 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.89 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.56→27.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1307 0 36 300 1643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061377
X-RAY DIFFRACTIONf_angle_d1.0371886
X-RAY DIFFRACTIONf_dihedral_angle_d29.121533
X-RAY DIFFRACTIONf_chiral_restr0.067218
X-RAY DIFFRACTIONf_plane_restr0.004236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.6370.25871230.23672567X-RAY DIFFRACTION98
1.637-1.73950.20091380.16742610X-RAY DIFFRACTION100
1.7395-1.87380.21751340.15512618X-RAY DIFFRACTION100
1.8738-2.06230.17751510.1452613X-RAY DIFFRACTION100
2.0623-2.36060.17471690.1492605X-RAY DIFFRACTION100
2.3606-2.97350.16711280.14822651X-RAY DIFFRACTION100
2.9735-27.44920.15251460.13132698X-RAY DIFFRACTION100
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)
10.07690.1050.0920.21750.02390.25070.0026-0.03180.00550.0288-0.0217-0.0109-0.02970.01940.01550.03510.0009-0.00560.0521-0.0050.036534.6194-5.07440.4583
20.0640.0522-0.10.0781-0.00870.3066-0.03830.0107-0.00250.00470.0099-0.0108-0.01630.03860.02390.02890.0094-0.01270.0458-0.00030.033725.5378-3.760929.8303
30.17520.0014-0.02090.1370.07660.0513-0.0142-0.00590.0207-0.0186-0.0020.01810.0292-0.03570.01740.02660.00280.00740.04640.00620.025222.8287-9.84322.4445
40.0222-0.0162-0.0180.01240.01440.0167-0.0158-0.0125-0.00970.0092-0.01110.0030.0196-0.0122-0.0314-0.00160.00380.01990.04660.0062-0.001126.2053-15.439632.469
50.1142-0.02710.00140.33920.20920.1322-0.0094-0.0278-0.00180.0454-0.0316-0.0168-0.0429-0.01810.04750.0387-0.0006-0.0020.05080.00190.033729.4259-8.653843.3083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 62:84)
2X-RAY DIFFRACTION2chain 'A' and (resseq 85:96)
3X-RAY DIFFRACTION3chain 'A' and (resseq 97:130)
4X-RAY DIFFRACTION4chain 'A' and (resseq 131:197)
5X-RAY DIFFRACTION5chain 'A' and (resseq 198:224)

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