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Basic information

Entry
Database: PDB / ID: 5ymt
TitleFunctional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / Rotavirus / P[19] VP8*
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 speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsSun, X. / 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_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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _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
G: Outer capsid protein VP4
H: Outer capsid protein VP4
I: Outer capsid protein VP4
J: Outer capsid protein VP4
K: Outer capsid protein VP4
L: Outer capsid protein VP4
M: Outer capsid protein VP4
N: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,83317
Polymers253,71014
Non-polymers2,1233
Water11,962664
1
A: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8302
Polymers18,1221
Non-polymers7081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8302
Polymers18,1221
Non-polymers7081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8302
Polymers18,1221
Non-polymers7081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.667, 131.667, 150.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Outer capsid protein VP4 / VP8*


Mass: 18122.115 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
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-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1a_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3-2/a4-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / 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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
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: 2.199→50 Å / Num. obs: 148275 / % possible obs: 99.9 % / Redundancy: 6 % / Net I/σ(I): 15.231

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJ6

5gj6


Resolution: 2.199→39.907 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.74
RfactorNum. reflection% reflection
Rfree0.2669 6659 5.01 %
Rwork0.2261 --
obs0.2281 132870 89.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.81 Å2 / Biso mean: 35.4422 Å2 / Biso min: 5.59 Å2
Refinement stepCycle: final / Resolution: 2.199→39.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17906 0 144 664 18714
Biso mean--54.03 33.92 -
Num. residues----2240
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)
10.2319-0.0514-0.04830.1383-0.0720.13430.00380.0091-0.06620.06760.01580.06930.0158-0.02990.05910.10160.0077-0.0060.08520.00350.0608-32.6933-37.255716.6802
20.09770.0308-0.08370.0861-0.07340.39110.12370.06690.0453-0.10380.03360.1042-0.1213-0.14590.59240.16180.047-0.01190.08930.0033-0.1583-50.2782-3.99193.2562
30.11730.0026-0.080.2531-0.110.1710.00590.0650.0304-0.10410.0037-0.12660.04690.07290.00310.1312-0.0012-0.00970.1265-0.00250.114-14.0333-27.63741.0909
40.18350.03470.12760.10060.05410.12760.0884-0.03720.03230.0959-0.071-0.1315-0.13410.02690.06610.2353-0.03510.00270.11130.00630.0985-29.28185.80115.3415
50.0706-0.0158-0.00610.06080.10570.19520.0021-0.0063-0.0256-0.1064-0.01650.1841-0.04660.0327-0.01150.19940.0108-0.04390.1301-0.0030.1-79.6887-4.8154.9415
60.10.14570.01760.14070.01960.1139-0.02020.11030.0479-0.0090.04380.13810.0951-0.00770.02760.2546-0.057-0.03310.12280.05360.2321-19.671131.4422-4.0783
70.1430.04140.1580.09010.06230.167-0.12490.10810.2105-0.0950.09780.2454-0.10020.06470.0010.1689-0.0099-0.00670.18760.07210.3016-48.5353-8.068947.6587
80.12890.06330.0210.0970.0260.08060.0363-0.0039-0.16720.00580.00380.06610.030.055600.1965-0.0070.00060.13560.03620.2794-32.62310.26766.4542
90.28350.09120.21750.0560.01750.22910.0084-0.22490.02850.04580.0237-0.28040.058-0.04490.00760.20490.0711-0.02430.1965-0.03430.3807-77.7676-8.970163.5133
100.1818-0.059-0.00660.0139-0.01240.1021-0.06470.3526-0.1975-0.01440.0264-0.00190.0220.0223-0.00020.16390.00040.00960.3076-0.03890.2959-51.247731.488949.3621
110.3661-0.07660.06920.41270.12320.21350.20530.19590.0664-0.1346-0.1833-0.06540.0395-0.0809-0.02490.25280.08110.01790.1555-0.02250.1186-62.263927.9536-0.0007
120.10210.05690.04890.1776-0.05160.119-0.02360.09080.29770.028-0.0753-0.1728-0.04230.2611-0.07990.15280.01080.03570.3320.11010.2966-9.7901-27.114948.4368
130.15620.0980.0040.1186-0.05450.02420.00710.10090.0645-0.10140.03010.0025-0.00230.047300.1852-0.0222-0.03220.1681-0.02950.2404-49.2961-57.4703-3.5175
14-0.0035-0.01950.00910.04740.05380.02780.0803-0.18980.39640.01670.0209-0.1343-0.10080.04570.00030.2873-0.07180.04820.2908-0.06480.3935-37.21591.1013-45.2265
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
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L
13X-RAY DIFFRACTION13chain M
14X-RAY DIFFRACTION14chain N

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