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Basic information

Entry
Database: PDB / ID: 6k2n
TitleStructural basis of glycan recognition in globally predominant human P[8] rotavirus
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / glycan binding specificity / VP8* structure / mucin core 2 / lacto-N-fucopentaose 1 (LNFP1)
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
Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDuan, Z. / Sun, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)no.2018ZA10711-001 and no.2017ZX10104001 China
CitationJournal: Virol Sin / Year: 2020
Title: Structural Basis of Glycan Recognition in Globally Predominant Human P[8] Rotavirus.
Authors: Sun, X. / Dang, L. / Li, D. / Qi, J. / Wang, M. / Chai, W. / Zhang, Q. / Wang, H. / Bai, R. / Tan, M. / Duan, Z.
History
DepositionMay 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 13, 2020Group: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Nov 22, 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
B: Outer capsid protein VP4
C: Outer capsid protein VP4
D: Outer capsid protein VP4
E: Outer capsid protein VP4
F: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0978
Polymers110,9246
Non-polymers1,1732
Water14,070781
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint0 kcal/mol
Surface area39650 Å2
Unit cell
Length a, b, c (Å)66.289, 114.550, 73.789
Angle α, β, γ (deg.)90.000, 95.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Outer capsid protein VP4


Mass: 18487.377 Da / Num. of mol.: 6 / Fragment: UNP residues 64-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: E2EA82
#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-alpha-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]DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_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
[][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}[(6+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium acetate trihydrate pH 4.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 99560 / % possible obs: 98.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.75 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 21.597
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 99560

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDB

5jdb


Resolution: 1.8→46.695 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.02
RfactorNum. reflection% reflection
Rfree0.2288 4273 4.93 %
Rwork0.2024 --
obs0.2037 86599 85.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.4 Å2 / Biso mean: 24.8501 Å2 / Biso min: 6.63 Å2
Refinement stepCycle: final / Resolution: 1.8→46.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7848 0 80 781 8709
Biso mean--59.77 34.4 -
Num. residues----960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058156
X-RAY DIFFRACTIONf_angle_d0.68911136
X-RAY DIFFRACTIONf_chiral_restr0.3531220
X-RAY DIFFRACTIONf_plane_restr0.0041448
X-RAY DIFFRACTIONf_dihedral_angle_d18.7422942
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7999-1.82030.2677820.26381484156647
1.8203-1.84180.3294890.26331685177452
1.8418-1.86420.26851050.25071758186356
1.8642-1.88780.2918960.2451869196558
1.8878-1.91270.2741900.23421984207462
1.9127-1.93890.26031020.2462053215564
1.9389-1.96660.2821090.2412197230668
1.9666-1.99590.26161130.22912268238171
1.9959-2.02710.22971070.23162381248875
2.0271-2.06030.25531230.22592470259376
2.0603-2.09590.30181270.22522648277582
2.0959-2.1340.27451330.22132770290386
2.134-2.1750.26071450.22432820296589
2.175-2.21940.27891780.21942941311992
2.2194-2.26770.2921840.21743034321896
2.2677-2.32040.24241610.21543100326197
2.3204-2.37850.24961970.21823157335499
2.3785-2.44280.21551660.21553173333999
2.4428-2.51460.23591470.22283164331199
2.5146-2.59580.24051610.212532193380100
2.5958-2.68860.25941790.219531973376100
2.6886-2.79620.23561490.222832333382100
2.7962-2.92340.21661610.213832093370100
2.9234-3.07750.23051630.190232233386100
3.0775-3.27030.20181720.19473175334799
3.2703-3.52270.21311380.183732593397100
3.5227-3.87710.19481540.169732433397100
3.8771-4.43770.17951770.155832033380100
4.4377-5.58960.18841860.17183203338999
5.5896-46.71080.24171790.21873206338598
Refinement TLS params.Method: refined / Origin x: -14.6553 Å / Origin y: 15.2505 Å / Origin z: -18.0265 Å
111213212223313233
T0.0984 Å2-0.0063 Å2-0.0005 Å2-0.0735 Å2-0.0013 Å2--0.0765 Å2
L0.5339 °2-0.0265 °2-0.0035 °2-0.0546 °20.0206 °2--0.0915 °2
S-0.0283 Å °-0.0145 Å °0.065 Å °0.0001 Å °0.0115 Å °0.0073 Å °-0.0111 Å °-0.0021 Å °-0.0145 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 160
2X-RAY DIFFRACTION1allB1 - 603
3X-RAY DIFFRACTION1allC1 - 160
4X-RAY DIFFRACTION1allD1 - 603
5X-RAY DIFFRACTION1allE1 - 160
6X-RAY DIFFRACTION1allF1 - 160
7X-RAY DIFFRACTION1allS1 - 781

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