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Basic information

Entry
Database: PDB / ID: 5yms
TitleStructural basis of glycan specificity and identification of a novel glycan binding cavity in human P[19] rotavirus
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / P[19] rotavirus / P[6] rotavirus / VP8* / Mucin core2core 2 / Lacto-N-tetrarosetetraose (LNT)
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 speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSun, X. / Dandi, L. / Duan, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81472003; 31500139;81601813; China
CitationJournal: J. Virol. / Year: 2018
Title: Glycan Binding Specificity and Mechanism of Human and Porcine P[6]/P[19] Rotavirus VP8*s.
Authors: Sun, X. / Li, D. / Qi, J. / Chai, W. / Wang, L. / Wang, L. / Peng, R. / Wang, H. / Zhang, Q. / Pang, L. / Kong, X. / Wang, H. / Jin, M. / Gao, G.F. / Duan, Z.
History
DepositionOct 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
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_unobs_or_zero_occ_atoms / 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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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
G: Outer capsid protein VP4
H: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,52716
Polymers146,0268
Non-polymers2,5008
Water17,691982
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4752
Polymers18,2531
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4752
Polymers18,2531
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4752
Polymers18,2531
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4752
Polymers18,2531
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4752
Polymers18,2531
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8402
Polymers18,2531
Non-polymers5871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4752
Polymers18,2531
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8402
Polymers18,2531
Non-polymers5871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.776, 129.346, 86.365
Angle α, β, γ (deg.)90.000, 116.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Outer capsid protein VP4 / rotavirus VP8* protein


Mass: 18253.311 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: P[19] VP8* and LNT / Source: (gene. exp.) Human rotavirus A
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9Q2P6
#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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 982 / 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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 30% w/v polyethylene glycol MME 5000

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 104019 / % possible obs: 99.9 % / Redundancy: 6.3 % / Net I/σ(I): 10.575
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.4 %

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJ6

5gj6


Resolution: 2.1→49.675 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 21.84
RfactorNum. reflection% reflection
Rfree0.213 4951 5.02 %
Rwork0.1812 --
obs0.1827 98627 94.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.41 Å2 / Biso mean: 31.9 Å2 / Biso min: 11.71 Å2
Refinement stepCycle: final / Resolution: 2.1→49.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10256 0 164 982 11402
Biso mean--58.6 36.76 -
Num. residues----1283
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)
10.5402-0.18510.13440.7839-0.11911.1698-0.03330.06250.00880.0386-0.0030.0146-0.1270.0884-00.1751-0.03540.02640.10550.00490.1541.295452.4932112.9311
20.9438-0.1297-0.47590.7255-0.12340.663-0.04710.0923-0.12750.0446-0.00220.0240.03850.0117-0.00110.1619-0.00110.00810.1162-0.03010.1505-17.736615.6814103.4046
30.97860.1768-0.01450.9135-0.02140.93340.0788-0.0267-0.0090.1715-0.021-0.01420.04690.114700.20240.0102-0.01030.1432-0.00420.1394.74633.3645130.7461
41.256-0.0124-0.49671.5043-0.33591.4321-0.0421-0.04960.0532-0.0395-0.0103-0.12580.0620.2246-0.00010.1576-0.00660.00990.2621-0.01520.1693-37.573715.2658146.5661
50.838-0.04130.11011.5990.02371.52630.04670.1216-0.0424-0.19130.0351-0.0072-0.0064-0.09630.00250.1932-0.0483-0.00190.2408-0.01320.1117-20.418553.0988155.1541
61.1568-0.5155-0.18971.0241-0.01991.0595-0.0147-0.14220.26240.07270.00430.049-0.0920.01380.00020.1787-0.0311-0.02060.2433-0.04040.2993-55.806333.7521144.2389
70.9460.1792-0.06380.7405-0.00480.88680.01830.03170.05620.0475-0.00650.0991-0.0562-0.025500.120.01360.0170.12170.00830.1826-33.991734.6839111.7586
80.9452-0.610.15271.2581-0.26711.35870.1243-0.1422-0.21580.01720.0494-0.16130.2178-0.06290.01690.2735-0.0614-0.0960.2821-0.01350.2633-7.512634.4833168.0752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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