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- PDB-3n7x: Crystal structure of Penaeus stylirostris densovirus capsid -

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Entry
Database: PDB / ID: 3n7x
TitleCrystal structure of Penaeus stylirostris densovirus capsid
ComponentsCapsid protein
KeywordsVIRUS / icosahedral virus capsid / virus-like particle / capsid protein / beta-barrel / parvovirus / brevidensovirus
Function / homologyInfectious hypodermal and haematopoietic necrosis virus, capsid protein / Infectious hypodermal and haematopoietic necrosis virus, capsid / Capsid protein
Function and homology information
Biological speciesInfectious hypodermal and hematopoietic necrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKaufmann, B. / Rossmann, M.G.
CitationJournal: J Virol / Year: 2010
Title: Structure of Penaeus stylirostris densovirus, a shrimp pathogen.
Authors: Bärbel Kaufmann / Valorie D Bowman / Yi Li / Jozsef Szelei / Peter J Waddell / Peter Tijssen / Michael G Rossmann /
Abstract: Penaeus stylirostris densovirus (PstDNV), a pathogen of penaeid shrimp, causes significant damage to farmed and wild shrimp populations. In contrast to other parvoviruses, PstDNV probably has only ...Penaeus stylirostris densovirus (PstDNV), a pathogen of penaeid shrimp, causes significant damage to farmed and wild shrimp populations. In contrast to other parvoviruses, PstDNV probably has only one type of capsid protein that lacks the phospholipase A2 activity that has been implicated as a requirement during parvoviral host cell infection. The structure of recombinant virus-like particles, composed of 60 copies of the 37.5-kDa coat protein, the smallest parvoviral capsid protein reported thus far, was determined to 2.5-Å resolution by X-ray crystallography. The structure represents the first near-atomic resolution structure within the genus Brevidensovirus. The capsid protein has a β-barrel "jelly roll" motif similar to that found in many icosahedral viruses, including other parvoviruses. The N-terminal portion of the PstDNV coat protein adopts a "domain-swapped" conformation relative to its twofold-related neighbor similar to the insect parvovirus Galleria mellonella densovirus (GmDNV) but in stark contrast to vertebrate parvoviruses. However, most of the surface loops have little structural resemblance to any of the known parvoviral capsid proteins.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Other
Revision 1.3Jul 16, 2014Group: Other
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Nov 27, 2019Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.6Dec 18, 2019Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6134
Polymers37,5241
Non-polymers893
Water2,864159
1
A: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)2,256,785240
Polymers2,251,46460
Non-polymers5,321180
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


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


  • icosahedral pentamer
  • 188 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)188,06520
Polymers187,6225
Non-polymers44315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 226 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)225,67824
Polymers225,1466
Non-polymers53218
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Capsid protein
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 1.13 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,128,392120
Polymers1,125,73230
Non-polymers2,66190
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)235.890, 245.471, 268.467
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.31094457, -0.82664326, -0.46901491), (0.78826883, 0.5, -0.35865244), (0.53098508, -0.25818903, 0.80708941)51.94709, 31.4205, 16.22486
3generate(-0.80397051, -0.54926736, -0.22789698), (0.44880324, -0.30901699, -0.83850065), (0.390137, -0.7764114, 0.49495352)34.51651, 82.25994, 48.79047
4generate(-0.80397051, 0.44880364, 0.39013699), (-0.54926687, -0.30901699, -0.77641071), (-0.22789698, -0.8385014, 0.49495352)-28.20327, 82.25994, 52.69227
5generate(0.31094457, 0.78826953, 0.53098509), (-0.82664252, 0.5, -0.2581888), (-0.46901492, -0.35865276, 0.8070894)-49.53565, 31.4205, 22.5381
6generate(-0.99228967, 0.12394034), (-1), (0.12394034, 0.99228967)125.682
7generate(-0.24273661, 0.78826953, 0.56542959), (-0.78826883, -0.5, 0.35865244), (0.56542959, -0.35865276, 0.74273661)-49.53565, 94.2615, 22.5381
8generate(0.84612535, 0.44880364, 0.28748453), (-0.44880324, 0.30901699, 0.83850065), (0.28748453, -0.8385014, 0.46289164)-28.20327, 43.42206, 52.69227
9generate(0.76952601, -0.54926736, -0.3257842), (0.54926687, 0.30901699, 0.77641071), (-0.32578421, -0.7764114, 0.53949098)34.51651, 43.42206, 48.79047
10generate(-0.36667696, -0.82664326, -0.42686008), (0.82664252, -0.5, 0.2581888), (-0.42686008, -0.25818903, 0.86667695)51.94709, 94.2615, 16.22486
11generate(-0.06197017, -0.06209, -0.99614483), (0.99807011, -0.06208994), (0.00385516, -0.998071, 0.06197017)3.9018, 62.841, 62.71978
12generate(-0.59715095, 0.2773759, -0.75264428), (0.27737565, -0.80901699, -0.5182219), (-0.75264428, -0.51822236, 0.40616794)-17.43058, 113.68044, 32.56561
13generate(-0.36667696, 0.82664326, -0.42686008), (-0.82664252, -0.5, -0.2581888), (-0.42686008, 0.25818903, 0.86667695)-51.94709, 94.2615, -16.22486
14generate(0.31094457, 0.82664326, -0.46901491), (-0.78826883, 0.5, 0.35865244), (0.53098508, 0.25818903, 0.80708941)-51.94709, 31.4205, -16.22486
15generate(0.49926373, 0.2773759, -0.82085224), (0.33946559, 0.80901699, 0.47984821), (0.79718174, -0.51822236, 0.30975326)-17.43058, 12.00156, 32.56561
16generate(-0.06197017, 0.06209, -0.99614483), (-0.99807011, 0.06208994), (0.00385516, 0.998071, 0.06197017)-3.9018, 62.841, -62.71978
17generate(-0.49926372, 0.3394659, -0.79718174), (-0.27737565, 0.80901699, 0.5182219), (0.82085224, 0.47984864, -0.30975326)-21.33238, 12.00156, -30.15417
18generate(-0.31094457, 0.78826953, -0.53098509), (0.82664252, 0.5, 0.2581888), (0.46901492, -0.35865276, -0.8070894)-49.53565, 31.4205, 22.5381
19generate(0.24273661, 0.78826953, -0.56542959), (0.78826883, -0.5, -0.35865244), (-0.56542959, -0.35865276, -0.74273661)-49.53565, 94.2615, 22.5381
20generate(0.39661126, 0.3394659, -0.85291412), (-0.33946559, -0.80901699, -0.47984821), (-0.85291412, 0.47984864, -0.20562825)-21.33238, 113.68044, -30.15417
21generate(-0.06197017, 0.998071, 0.00385516), (-0.06208994, -0.99807011), (-0.99614483, -0.06209, 0.06197017)-62.71978, 62.841, 3.9018
22generate(0.76952601, 0.54926736, -0.3257842), (-0.54926687, 0.30901699, -0.77641071), (-0.32578421, 0.7764114, 0.53949098)-34.51651, 43.42206, -48.79047
23generate(0.49926373, -0.2773759, -0.82085224), (-0.33946559, 0.80901699, -0.47984821), (0.79718174, 0.51822236, 0.30975326)17.43058, 12.00156, -32.56561
24generate(-0.49926372, -0.3394659, -0.79718174), (0.27737565, 0.80901699, -0.5182219), (0.82085224, -0.47984864, -0.30975326)21.33238, 12.00156, 30.15417
25generate(-0.84612535, 0.44880364, -0.28748453), (0.44880324, 0.30901699, -0.83850065), (-0.28748453, -0.8385014, -0.46289164)-28.20327, 43.42206, 52.69227
26generate(0.06197017, 0.998071, -0.00385516), (0.06208994, 0.99807011), (0.99614483, -0.06209, -0.06197017)-62.71978, 62.841, 3.9018
27generate(0.80397051, 0.44880364, -0.39013699), (0.54926687, -0.30901699, 0.77641071), (0.22789698, -0.8385014, -0.49495352)-28.20327, 82.25994, 52.69227
28generate(0.39661126, -0.3394659, -0.85291412), (0.33946559, -0.80901699, 0.47984821), (-0.85291412, -0.47984864, -0.20562825)21.33238, 113.68044, 30.15417
29generate(-0.59715095, -0.2773759, -0.75264428), (-0.27737565, -0.80901699, 0.5182219), (-0.75264428, 0.51822236, 0.40616794)17.43058, 113.68044, -32.56561
30generate(-0.80397051, 0.54926736, -0.22789698), (-0.44880324, -0.30901699, 0.83850065), (0.390137, 0.7764114, 0.49495352)-34.51651, 82.25994, -48.79047

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Components

#1: Protein Capsid protein


Mass: 37524.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious hypodermal and hematopoietic necrosis virus
Gene: capsid protein / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q9E2G5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5% PEG8000, 10mM Tris-HCl, 5% glycerol, starting protein concentration in drop 7mg/ml, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2006
Details: 300x300 mm2 active area, ~2.2sec read-time, 4096x4096 of 0.072mm pixels
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 896125 / Num. obs: 338268 / % possible obs: 64.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.107 / Χ2: 1.291 / Net I/σ(I): 12.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.35 / Num. unique all: 23750 / Rsym value: 0.598 / Χ2: 2.093 / % possible all: 45.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
envelopephasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRYO-ELECTRON MICROSCOPY RECONSTRUCTION

Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 6725 1.3 %random
Rwork0.278 ---
all0.278 337569 --
obs0.278 337569 63.4 %-
Solvent computationBsol: 17.203 Å2
Displacement parametersBiso max: 63.44 Å2 / Biso mean: 25.686 Å2 / Biso min: 5.78 Å2
Baniso -1Baniso -2Baniso -3
1-6.124 Å20 Å20 Å2
2---4.377 Å20 Å2
3----1.748 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 3 159 2558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.412
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection
Rfree0.3829 414
Rwork0.3812 -
obs-20378

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