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- PDB-4zpy: Structure of N170A MVM mutant empty capsid -

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Basic information

Entry
Database: PDB / ID: 4zpy
TitleStructure of N170A MVM mutant empty capsid
ComponentsVP1 protein
KeywordsVIRUS / minute virus of mice / empty capsid / N170A mutant
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Capsid protein VP1 / VP1 protein
Similarity search - Component
Biological speciesMurine minute virus strain MVM prototype
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsGuerra, P. / Querol-Audi, J. / Silva, C. / Mateu, M.G. / Verdaguer, N.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis for biologically relevant mechanical stiffening of a virus capsid by cavity-creating or spacefilling mutations.
Authors: Guerra, P. / Valbuena, A. / Querol-Audi, J. / Silva, C. / Castellanos, M. / Rodriguez-Huete, A. / Garriga, D. / Mateu, M.G. / Verdaguer, N.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1 protein


Theoretical massNumber of molelcules
Total (without water)61,2031
Polymers61,2031
Non-polymers00
Water0
1
A: VP1 protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,672,18360
Polymers3,672,18360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation54
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation3_545-x+y,-x-1,z1
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1 protein
x 5


  • icosahedral pentamer
  • 306 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)306,0155
Polymers306,0155
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1 protein
x 6


  • icosahedral 23 hexamer
  • 367 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)367,2186
Polymers367,2186
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
Unit cell
Length a, b, c (Å)410.190, 410.190, 559.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.3077, -0.179, 0.9345), (0.1751, 0.976, 0.1293), (-0.9352, 0.1238, 0.3317)44.92, 6.323, -32.7
3generate(-0.8094, -0.1132, 0.5762), (0.1061, 0.9369, 0.333), (-0.5776, 0.3307, -0.7464)27.3, 16.06, -84.46
4generate(-0.8098, 0.1104, -0.5762), (-0.1106, 0.9358, 0.3348), (0.5762, 0.3348, -0.7456)-27.66, 16.18, -83.83
5generate(0.3074, 0.1803, -0.9343), (-0.1819, 0.9749, 0.1283), (0.934, 0.1305, 0.3325)-44.78, 6.083, -31.71
6generate(-1, -0.001495, 0.000641), (-0.001541, 0.7447, -0.6674), (0.000521, -0.6674, -0.7447)-0.1185, -122.8, -320.9
7generate(-0.311, 0.1797, -0.9333), (0.7539, 0.6446, -0.1271), (0.5787, -0.7431, -0.336)-44.7, -96.31, -301
8generate(0.8089, 0.1133, -0.5769), (0.465, 0.4771, 0.7458), (0.3597, -0.8715, 0.3333)-27.33, -54.36, -268.6
9generate(0.8085, -0.1109, 0.5779), (-0.4682, 0.4737, 0.7459), (-0.3565, -0.8737, 0.3311)27.72, -54.78, -269.3
10generate(-0.3104, -0.1826, 0.9329), (-0.7586, 0.639, -0.1273), (-0.5728, -0.7472, -0.3369)44.25, -97.12, -301.6
11generate(-1, -0.003132, 0.000154), (0.003132, -1, 0.000359), (0.000153, 0.00036, 1)-0.3968, -236.7, 93.49
12generate(-0.31, 0.1806, -0.9334), (-0.1758, -0.9757, -0.1304), (-0.9343, 0.1237, 0.3342)-44.62, -243.3, 60.93
13generate(0.8091, 0.1126, -0.5768), (-0.1069, -0.9369, -0.3328), (-0.5779, 0.331, -0.746)-27.43, -252.9, 9.003
14generate(0.8096, -0.1129, 0.576), (0.1089, -0.9354, -0.3364), (0.5768, 0.3351, -0.745)27.34, -253.1, 9.654
15generate(-0.3097, -0.1807, 0.9335), (0.1823, -0.9749, -0.1282), (0.9332, 0.1304, 0.3349)44.6, -242.9, 61.87
16generate(1, 0.002478, -0.000541), (0.002206, -0.745, 0.6671), (0.00125, -0.6671, -0.745)0.3021, -114, -227.6
17generate(0.3103, -0.1778, 0.9339), (-0.7535, -0.645, 0.1276), (0.5797, -0.7432, -0.3341)45.04, -140.5, -207.5
18generate(-0.8085, -0.1127, 0.5777), (-0.4658, -0.4776, -0.745), (0.3598, -0.8713, 0.3336)27.55, -182.5, -175.3
19generate(-0.8092, 0.1083, -0.5774), (0.4685, -0.4741, -0.7455), (-0.3545, -0.8738, 0.3329)-28.05, -182.1, -175.8
20generate(0.3096, 0.1804, -0.9336), (0.7582, -0.6394, 0.1278), (-0.5738, -0.7474, -0.3348)-44.63, -139.7, -208.1

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Components

#1: Protein VP1 protein / Capsid protein VP1 / Coat protein VP1


Mass: 61203.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine minute virus strain MVM prototype
Gene: VP1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q84367, UniProt: P03137*PLUS

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MPD, NaCl, NaAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9787 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.8→49.93 Å / Num. obs: 176252 / % possible obs: 99.8 % / Redundancy: 10.5 % / CC1/2: 0.982 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
3.8-3.879.90.7892.40.766197.7
20.81-49.9310.30.07624.50.985193

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
PHASERphasing
DMphasing
CNSrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z14

1z14


Resolution: 3.8→49.9 Å
RfactorNum. reflection
Rfree0.2891 -
Rwork0.2825 -
obs-345341
Refinement stepCycle: LAST / Resolution: 3.8→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4314 0 0 0 4314

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