[English] 日本語
Yorodumi
- PDB-2qqp: Crystal Structure of Authentic Providence Virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qqp
TitleCrystal Structure of Authentic Providence Virus
Components
  • (p81) x 2
  • RNA (5'-R(*UP*UP*UP*U)-3')
KeywordsVIRUS / capsid / coat protein / protein-RNA complex / beta barrel / Ig-like domain / tetravirus / tetraviridae / icosahedral virus / quasiequivalence / auto-catalytic cleavage / auto proteolysis
Function / homology
Function and homology information


T=3 icosahedral viral capsid / identical protein binding / metal ion binding
Similarity search - Function
Immunoglobulin-like - #4260 / Helix Hairpins - #650 / V-type ATP synthase subunit C fold / V-type ATP synthase subunit C fold - #10 / V-type ATP synthase subunit C fold - #20 / V-type ATP synthase subunit C fold / Peptidase N2 / Peptidase family A21 / Jelly Rolls - #20 / Helix Hairpins ...Immunoglobulin-like - #4260 / Helix Hairpins - #650 / V-type ATP synthase subunit C fold / V-type ATP synthase subunit C fold - #10 / V-type ATP synthase subunit C fold - #20 / V-type ATP synthase subunit C fold / Peptidase N2 / Peptidase family A21 / Jelly Rolls - #20 / Helix Hairpins / Helix non-globular / Special / Viral coat protein subunit / Jelly Rolls / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesProvidence virus
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsSpeir, J.A. / Taylor, D.J. / Johnson, J.E.
Citation
Journal: Structure / Year: 2010
Title: Evolution in action: N and C termini of subunits in related T = 4 viruses exchange roles as molecular switches.
Authors: Speir, J.A. / Taylor, D.J. / Natarajan, P. / Pringle, F.M. / Ball, L.A. / Johnson, J.E.
#1: Journal: Virology / Year: 2003
Title: Providence virus: a new member of the Tetraviridae that infects cultured insect cells
Authors: Pringle, F.M. / Johnson, K.N. / Goodman, C.L. / McIntosh, A.H. / Ball, L.A.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_nat / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_ref / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_ncbi_taxonomy_id / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: p81
B: p81
C: p81
D: p81
E: p81
F: p81
G: p81
H: p81
R: RNA (5'-R(*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,83711
Polymers273,7569
Non-polymers802
Water1086
1
A: p81
B: p81
C: p81
D: p81
E: p81
F: p81
G: p81
H: p81
R: RNA (5'-R(*UP*UP*UP*U)-3')
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)16,430,199660
Polymers16,425,389540
Non-polymers4,809120
Water4,324240
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: p81
B: p81
C: p81
D: p81
E: p81
F: p81
G: p81
H: p81
R: RNA (5'-R(*UP*UP*UP*U)-3')
hetero molecules
x 5


  • icosahedral pentamer
  • 1.37 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)1,369,18355
Polymers1,368,78245
Non-polymers40110
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: p81
B: p81
C: p81
D: p81
E: p81
F: p81
G: p81
H: p81
R: RNA (5'-R(*UP*UP*UP*U)-3')
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.64 MDa, 54 polymers
Theoretical massNumber of molelcules
Total (without water)1,643,02066
Polymers1,642,53954
Non-polymers48112
Water43224
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: p81
B: p81
C: p81
D: p81
E: p81
F: p81
G: p81
H: p81
R: RNA (5'-R(*UP*UP*UP*U)-3')
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 8.22 MDa, 270 polymers
Theoretical massNumber of molelcules
Total (without water)8,215,099330
Polymers8,212,695270
Non-polymers2,40560
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)659.790, 434.070, 415.850
Angle α, β, γ (deg.)90.000, 126.130, 90.000
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.32321316, -0.74537992, 0.58304548), (0.84951879, 0.5, 0.16827899), (-0.41695452, 0.44091811, 0.79482083)
3generate(-0.77185095, -0.35653125, 0.52643288), (0.62917036, -0.30901699, 0.71319923), (-0.09160111, 0.88169948, 0.46283396)
4generate(-0.77185095, 0.62917037, -0.09160111), (-0.35653125, -0.30901699, 0.88169947), (0.52643288, 0.71319924, 0.46283396)
5generate(0.32321316, 0.8495188, -0.41695452), (-0.74537992, 0.5, 0.44091811), (0.58304548, 0.16827899, 0.79482083)
6generate(-0.94321534, 0.33218192), (-1), (0.33218192, 0.94321534)
7generate(-0.44336436, 0.8495188, -0.28591233), (-0.84951879, -0.5, -0.16827899), (-0.28591233, 0.16827899, 0.94336436)
8generate(0.69759342, 0.62917037, -0.3427945), (-0.62917036, 0.30901699, -0.71319923), (-0.3427945, 0.71319924, 0.61142357)
9generate(0.90289314, -0.35653125, 0.24014464), (0.35653125, 0.30901699, -0.88169947), (0.24014464, 0.88169948, 0.40612386)
10generate(-0.11118244, -0.74537992, 0.65730301), (0.74537992, -0.5, -0.44091811), (0.65730301, 0.44091811, 0.61118244)
11generate(0.16609096, 0.16850024, 0.97160767), (0.98570161, -0.16850024), (-0.02839233, 0.98570162, -0.16609096)
12generate(-0.20828931, 0.38884867, 0.89744765), (0.38884867, -0.80901699, 0.44078137), (0.89744765, 0.44078137, 0.0173063)
13generate(-0.11118244, 0.74537992, 0.65730301), (-0.74537992, -0.5, 0.44091811), (0.65730301, -0.44091811, 0.61118244)
14generate(0.32321316, 0.74537992, 0.58304548), (-0.84951879, 0.5, -0.16827899), (-0.41695452, -0.44091811, 0.79482083)
15generate(0.49457755, 0.38884867, 0.77729644), (0.22034843, 0.80901699, -0.54492024), (-0.84073754, 0.44078137, 0.31443945)
16generate(0.16609096, -0.16850024, 0.97160767), (-0.98570161, 0.16850024), (-0.02839233, -0.98570162, -0.16609096)
17generate(-0.49457755, 0.22034843, 0.84073754), (-0.38884867, 0.80901699, -0.44078137), (-0.77729644, -0.54492025, -0.31443945)
18generate(-0.32321316, 0.8495188, 0.41695452), (0.74537992, 0.5, -0.44091811), (-0.58304548, 0.16827899, -0.79482083)
19generate(0.44336436, 0.8495188, 0.28591233), (0.84951879, -0.5, 0.16827899), (0.28591233, 0.16827899, -0.94336436)
20generate(0.74577094, 0.22034843, 0.62870683), (-0.22034843, -0.80901699, 0.54492024), (0.62870683, -0.54492025, -0.55478793)
21generate(0.16609096, 0.98570162, -0.02839233), (0.16850024, 0.98570161), (0.97160767, -0.16850024, -0.16609096)
22generate(0.90289314, 0.35653125, 0.24014464), (-0.35653125, 0.30901699, 0.88169947), (0.24014464, -0.88169948, 0.40612386)
23generate(0.49457755, -0.38884867, 0.77729644), (-0.22034843, 0.80901699, 0.54492024), (-0.84073754, -0.44078137, 0.31443945)
24generate(-0.49457755, -0.22034843, 0.84073754), (0.38884867, 0.80901699, 0.44078137), (-0.77729644, 0.54492025, -0.31443945)
25generate(-0.69759342, 0.62917037, 0.3427945), (0.62917036, 0.30901699, 0.71319923), (0.3427945, 0.71319924, -0.61142357)
26generate(-0.16609096, 0.98570162, 0.02839233), (-0.16850024, -0.98570161), (-0.97160767, -0.16850024, 0.16609096)
27generate(0.77185095, 0.62917037, 0.09160111), (0.35653125, -0.30901699, -0.88169947), (-0.52643288, 0.71319924, -0.46283396)
28generate(0.74577094, -0.22034843, 0.62870683), (0.22034843, -0.80901699, -0.54492024), (0.62870683, 0.54492025, -0.55478793)
29generate(-0.20828931, -0.38884867, 0.89744765), (-0.38884867, -0.80901699, -0.44078137), (0.89744765, -0.44078137, 0.0173063)
30generate(-0.77185095, 0.35653125, 0.52643288), (-0.62917036, -0.30901699, -0.71319923), (-0.09160111, -0.88169948, 0.46283396)
DetailsDeposited coord. are the asym. unit of an icosahedral virus capsid. The crystal asym. unit contains 30 copies of deposited coord. (half virus capsid). Biological unit is an icosahedral virus particle, which contains 60 copies of deposited coord.

-
Components

#1: Protein
p81


Mass: 60696.430 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: corn earworm, Lepidoptera, Noctuidae, MG8 (mid gut) cell line
Source: (natural) Providence virus / Strain: BCIRL-HZ / References: UniProt: Q80IX5
#2: Protein
p81


Mass: 7447.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: corn earworm, Lepidoptera, Noctuidae, MG8 (mid gut) cell line
Source: (natural) Providence virus / Strain: BCIRL-HZ / References: UniProt: Q80IX5
#3: RNA chain RNA (5'-R(*UP*UP*UP*U)-3')


Mass: 1179.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 ul of 7mg/ml virus solution (20mM Tris pH 7.5) added to 2 ul of 100mM Tris pH 7.5, 0.5-1.5% PEG8000, 10-100mM NaCl. Plates about 0.1 mm in size appear in 1-4 weeks., vapor diffusion, ...Details: 2 ul of 7mg/ml virus solution (20mM Tris pH 7.5) added to 2 ul of 100mM Tris pH 7.5, 0.5-1.5% PEG8000, 10-100mM NaCl. Plates about 0.1 mm in size appear in 1-4 weeks., vapor diffusion, hanging drop, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
120mM Tris11
2100mM Tris12
3PEG800012
4NaCl12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 3.6 / Number: 354357 / Rmerge(I) obs: 0.158 / Χ2: 0.91 / D res high: 3.8 Å / D res low: 50 Å / Num. obs: 272211 / % possible obs: 29.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
8.18502910.0721.213
6.498.183010.1480.95
5.676.4929.710.190.792
5.165.6730.110.1860.811
4.795.1630.410.1750.849
4.54.793010.1710.861
4.284.529.910.1790.856
4.094.2829.810.1960.834
3.944.0928.710.2160.764
3.83.9428.210.2490.755
ReflectionResolution: 3.8→50 Å / Num. obs: 272211 / % possible obs: 29.6 % / Observed criterion σ(I): -0.5 / Redundancy: 1.3 % / Rmerge(I) obs: 0.158 / Χ2: 0.906 / Net I/σ(I): 3.6
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 1.9 / Num. unique all: 25858 / Χ2: 0.755 / % possible all: 28.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ohf

1ohf


Resolution: 3.8→49.42 Å / Data cutoff high absF: 54374.6 / Data cutoff high rms absF: 54374.6 / Data cutoff low absF: 0 / Cross valid method: not used / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Subunit A in the publication is represented by chains A and B; subunit B is represented by chains C and D; subunit C is represented by chains E and F; and subunit D is represented by chains ...Details: Subunit A in the publication is represented by chains A and B; subunit B is represented by chains C and D; subunit C is represented by chains E and F; and subunit D is represented by chains G and H. Cross-validation not used due to 30-fold non-crystallographic symmetry.
RfactorNum. reflection% reflectionSelection details
Rwork0.285 ---
all0.285 263822 --
obs0.285 263822 28.6 %-
Rfree---not used
Solvent computationSolvent model: flat / Bsol: 0.52 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 20.945 Å2
Baniso -1Baniso -2Baniso -3
1--5.452 Å20 Å2-3.085 Å2
2--6.198 Å20 Å2
3----0.746 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.55 Å
Refinement stepCycle: LAST / Resolution: 3.8→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16549 77 2 6 16634
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it0.9591.5
X-RAY DIFFRACTIONc_scbond_it1.2512
X-RAY DIFFRACTIONc_mcangle_it1.6292
X-RAY DIFFRACTIONc_scangle_it2.0682.5
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used% reflection obs (%)
3.8-3.970.3093X-RAY DIFFRACTION29998826.1
3.97-4.180.2913X-RAY DIFFRACTION337328
4.18-4.440.2821X-RAY DIFFRACTION333908
4.44-4.790.2715X-RAY DIFFRACTION340558
4.79-5.270.2715X-RAY DIFFRACTION334788
5.27-6.030.2891X-RAY DIFFRACTION335468
6.03-7.590.2791X-RAY DIFFRACTION320928
7.59-49.420.2825X-RAY DIFFRACTION299988
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more