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- PDB-7uzt: Crystal structure of the human astrovirus MLB1 capsid protein spi... -

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Basic information

Entry
Database: PDB / ID: 7uzt
TitleCrystal structure of the human astrovirus MLB1 capsid protein spike domain at 1.86-A resolution
ComponentsCapsid polyprotein VP90
KeywordsVIRAL PROTEIN / capsid protein / spike domain / projection domain
Function / homologyTurkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / Capsid polyprotein VP90
Function and homology information
Biological speciesAstrovirus MLB1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsDelgado-Cunningham, K. / DuBois, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI144090 United States
CitationJournal: Structure / Year: 2022
Title: Structure of the divergent human astrovirus MLB capsid spike.
Authors: Delgado-Cunningham, K. / Lopez, T. / Khatib, F. / Arias, C.F. / DuBois, R.M.
History
DepositionMay 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid polyprotein VP90
B: Capsid polyprotein VP90
C: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)88,9253
Polymers88,9253
Non-polymers00
Water4,161231
1
A: Capsid polyprotein VP90

A: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)59,2832
Polymers59,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3170 Å2
ΔGint-25 kcal/mol
Surface area16210 Å2
MethodPISA
2
B: Capsid polyprotein VP90

B: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)59,2832
Polymers59,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3140 Å2
ΔGint-31 kcal/mol
Surface area15900 Å2
MethodPISA
3
C: Capsid polyprotein VP90

C: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)59,2832
Polymers59,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3240 Å2
ΔGint-30 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.100, 77.109, 75.445
Angle α, β, γ (deg.)90.000, 110.710, 90.000
Int Tables number3
Space group name H-MP121
Symmetry operation#1: x,y,z
#2: -x,y,-z
Components on special symmetry positions
IDModelComponents
11B-748-

HOH

21B-767-

HOH

31C-722-

HOH

41C-747-

HOH

51C-762-

HOH

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Components

#1: Protein Capsid polyprotein VP90


Mass: 29641.523 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Astrovirus MLB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B6UYJ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-tris-HCl pH 5.5, 22.5% w/v polyethylene glycol 3350, 0.35 M magnesium chloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
401N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.211.00004
SYNCHROTRONALS 5.0.24
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELJun 5, 2021
DECTRIS PILATUS3 6M4PIXELJun 5, 2021
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
4SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.000041
21
ReflectionResolution: 1.86→47.66 Å / Num. obs: 63807 / % possible obs: 98.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.95 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.052 / Rrim(I) all: 0.097 / Net I/σ(I): 8.7 / Num. measured all: 219235 / Scaling rejects: 156
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.86-1.93.30.4331262637880.8840.2740.5142.794.2
9.11-47.663.40.03920285890.9980.0240.04616.498.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
BOSdata collection
XDSFebruary 5, 2021data reduction
Aimless0.7.7.data scaling
Coot0.9.5model building
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→47.66 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 2015 3.16 %
Rwork0.2417 61779 -
obs0.2423 63794 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.16 Å2 / Biso mean: 22.5145 Å2 / Biso min: 6.01 Å2
Refinement stepCycle: final / Resolution: 1.86→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5024 0 0 231 5255
Biso mean---26.08 -
Num. residues----639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.910.32661450.28674285443095
1.91-1.960.29811500.25994325447597
1.96-2.010.29871390.25524340447997
2.01-2.080.30631350.24334384451997
2.08-2.150.2661430.2334416455998
2.15-2.240.24911420.2414352449498
2.24-2.340.26951490.2384414456398
2.34-2.470.28171350.25974396453198
2.47-2.620.2831380.25394427456598
2.62-2.820.28621460.26234409455598
2.82-3.110.2711500.25674464461499
3.11-3.560.26731430.23754468461199
3.56-4.480.21161490.21684515466499
4.48-47.660.22941510.23134584473599

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