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- PDB-5vx8: VP8* of P[6] Human Rotavirus RV3 -

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Basic information

Entry
Database: PDB / ID: 5vx8
TitleVP8* of P[6] Human Rotavirus RV3
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / Glycan / HBGA / rotavirus
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
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 Å
AuthorsHu, L. / Venkataram Prasad, B.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36040 United States
Robert A. Welch FoundationQ1279 United States
CitationJournal: Nat Commun / Year: 2018
Title: Glycan recognition in globally dominant human rotaviruses.
Authors: Hu, L. / Sankaran, B. / Laucirica, D.R. / Patil, K. / Salmen, W. / Ferreon, A.C.M. / Tsoi, P.S. / Lasanajak, Y. / Smith, D.F. / Ramani, S. / Atmar, R.L. / Estes, M.K. / Ferreon, J.C. / Prasad, B.V.V.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1594
Polymers36,9672
Non-polymers1922
Water6,413356
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5802
Polymers18,4831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5802
Polymers18,4831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.790, 43.100, 65.740
Angle α, β, γ (deg.)94.86, 99.40, 90.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Outer capsid protein VP4 / Rotavirus RV3 VP8*


Mass: 18483.477 Da / Num. of mol.: 2 / Fragment: UNP residues 65-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D7F7M7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.7 M ammonium sulfate, 0.1 M Tris, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2013
RadiationMonochromator: Single crystal, cylindrically bent Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2→27.41 Å / Num. obs: 33614 / % possible obs: 90.5 % / Redundancy: 2.1 % / CC1/2: 0.986 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.8
Reflection shellHighest resolution: 2 Å / Rmerge(I) obs: 0.102 / CC1/2: 0.947

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Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
iMOSFLM7.0.9data reduction
SCALA3.3.21data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AEN

2aen


Resolution: 2→27.41 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.23
RfactorNum. reflection% reflection
Rfree0.2579 925 5.06 %
Rwork0.2081 --
obs0.2107 18332 83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 10 356 2958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042670
X-RAY DIFFRACTIONf_angle_d0.6943642
X-RAY DIFFRACTIONf_dihedral_angle_d5.0511560
X-RAY DIFFRACTIONf_chiral_restr0.048408
X-RAY DIFFRACTIONf_plane_restr0.004460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05890.279910.21472148X-RAY DIFFRACTION66
2.0589-2.12540.29451450.22382744X-RAY DIFFRACTION85
2.1254-2.20130.31371000.22322710X-RAY DIFFRACTION86
2.2013-2.28940.37781230.28362491X-RAY DIFFRACTION77
2.2894-2.39350.27811470.23882739X-RAY DIFFRACTION86
2.3935-2.51960.29831660.20972826X-RAY DIFFRACTION87
2.5196-2.67740.25091780.21582663X-RAY DIFFRACTION86
2.6774-2.88390.24121630.2162750X-RAY DIFFRACTION87
2.8839-3.17370.24671390.2042769X-RAY DIFFRACTION86
3.1737-3.63210.2591550.18782720X-RAY DIFFRACTION85
3.6321-4.57260.20151280.17242668X-RAY DIFFRACTION83
4.5726-27.4150.21471670.18782684X-RAY DIFFRACTION84
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)
10.0330.0190.01540.053-0.03610.0546-0.00320.00170.005-0.0365-0.00940.00050.02490.0177-0.06180.05120.0335-0.00930.0177-0.00220.011328.548230.618860.8576
20.19850.0337-0.06080.0638-0.00470.031-0.0024-0.0592-0.0325-0.0021-0.0117-0.00790.02120.028-0.01030.02490.00770.00670.0121-0.00080.020730.679818.571871.3579
30.0583-0.02240.01710.0106-0.00520.0056-0.0145-0.00020.03-0.00390.0074-0.06120.00260.0658-0.0165-0.0130.00350.00940.05420.01350.037937.865933.772269.5597
40.0466-0.00450.01680.0301-0.03050.0345-0.02920.03210.01710.0243-0.0166-0.02450.00260.0199-0.12880.0747-0.02730.02980.0180.08940.049329.68679.029151.4361
50.10160.0202-0.02070.058-0.03040.01940.00240.02170.01030.03340.00480.0018-0.00980.003-0.00310.0295-0.0063-0.00060.01240.00030.043429.8284-0.591444.4125
60.0139-0.00160.00650.0021-0.00260.00820.04130.0733-0.0389-0.0458-0.00080.0250.0680.0068-0.00030.0672-0.0146-0.02320.1141-0.02690.036336.2874-8.853434.4944
70.14660.11580.09350.14130.030.1524-0.06960.10130.0016-0.09370.02650.0049-0.04810.0551-0.01440.07770.0064-0.00470.0752-0.01390.044127.6902-3.766732.5878
80.0250.0340.03030.04260.03790.0347-0.04280.02560.018-0.03770.00110.0328-0.0192-0.0149-0.06780.0771-0.05020.01230.0378-0.01320.039725.9572-10.141340.6193
90.03270.06930.05870.14820.12460.1048-0.00140.01620.02120.0431-0.06640.063-0.0093-0.0324-0.0430.05460.00430.01810.06330.04050.075323.71914.942242.1733
100.0072-0.0078-0.01420.03850.08260.254-0.01620.02270.00410.0471-0.05960.016-0.0433-0.0904-0.06080.0448-0.02430.00910.0767-0.00310.046121.6403-0.394146.0083
110.09520.03540.02190.0226-0.00150.1189-0.0188-0.00220.03780.01830.06040.0888-0.0434-0.03240.02280.03930.0232-0.01630.04460.01970.130920.334712.192942.7122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 65 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 203 )
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 223 )
4X-RAY DIFFRACTION4chain 'B' and (resid 65 through 79 )
5X-RAY DIFFRACTION5chain 'B' and (resid 80 through 108 )
6X-RAY DIFFRACTION6chain 'B' and (resid 109 through 130 )
7X-RAY DIFFRACTION7chain 'B' and (resid 131 through 144 )
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 159 )
9X-RAY DIFFRACTION9chain 'B' and (resid 160 through 169 )
10X-RAY DIFFRACTION10chain 'B' and (resid 170 through 203 )
11X-RAY DIFFRACTION11chain 'B' and (resid 204 through 223 )

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