[English] 日本語
Yorodumi
- PDB-5l7o: X-ray structure of Triatoma virus empty capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l7o
TitleX-ray structure of Triatoma virus empty capsid
Components(Capsid proteinCapsid) x 3
KeywordsVIRUS / Dicistroviridae / RNA release / uncoating / capsid disassembly
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Jelly Rolls - #20 / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTriatoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSanchez-Eugenia, R.
CitationJournal: J.Gen.Virol. / Year: 2016
Title: X-ray structure of Triatoma virus empty capsid: insights into the mechanism of uncoating and RNA release in dicistroviruses.
Authors: Sanchez-Eugenia, R. / Durana, A. / Lopez-Marijuan, I. / Marti, G.A. / Guerin, D.M.
History
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)90,1943
Polymers90,1943
Non-polymers00
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,411,634180
Polymers5,411,634180
Non-polymers00
Water0
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
B: Capsid protein
C: Capsid protein
x 5


  • icosahedral pentamer
  • 451 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)450,96915
Polymers450,96915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 541 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)541,16318
Polymers541,16318
Non-polymers00
Water0
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
Unit cell
Length a, b, c (Å)305.586, 305.586, 796.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.48017, 0.63598, -0.60412), (-0.87537, 0.39161, -0.28351), (0.05627, 0.66496, 0.74476)-106.59795, -66.37648, -37.86388
3generate(0.48005, -0.87546, 0.05582), (0.63715, 0.3917, 0.66378), (-0.60298, -0.28308, 0.74584)-4.89949, 119.00974, -54.87138
4generate(-0.35885, 0.15286, -0.92079), (-0.77892, -0.59261, 0.20519), (-0.51431, 0.79085, 0.33172)-176.95657, 11.66932, -116.35278
5generate(-0.36031, -0.77986, -0.51185), (0.1556, -0.59127, 0.79132), (-0.91976, 0.20548, 0.33438)-114.27019, 126.2333, -126.57966
6generate(0.42838, 0.67332, 0.6026), (0.67332, -0.68261, 0.28406), (0.60261, 0.28405, -0.74578)-23.03971, 149.21181, -114.58199
7generate(0.04632, -0.38384, -0.92224), (0.9019, -0.38084, 0.20381), (-0.42945, -0.84121, 0.32855)-67.93536, 249.60408, 40.52315
8generate(-0.60835, -0.60467, 0.51408), (-0.60924, -0.05934, -0.79076), (0.50865, -0.79426, -0.33229)-64.04205, -50.08199, -53.30259
9generate(-0.49227, 0.70283, -0.51351), (-0.58968, 0.16467, 0.79067), (0.64027, 0.69203, 0.33338)-265.48297, -54.12281, 68.56548
10generate(0.51987, 0.85237, 0.05651), (-0.65518, 0.35541, 0.66666), (0.54816, -0.3836, 0.74322)-151.32704, -74.94608, 129.61537
11generate(0.8554, 0.07765, -0.51212), (0.43373, 0.43309, 0.79013), (0.28315, -0.898, 0.33679)-4.3089, 78.39626, 154.75473
12generate(0.33202, 0.07101, -0.9406), (0.06762, -0.99639, -0.05135), (-0.94085, -0.04656, -0.33562)-63.42841, 188.65059, -75.43155
13generate(0.3129, 0.22947, -0.92165), (-0.12192, 0.97205, 0.20063), (0.94193, 0.04959, 0.33214)-81.29114, -26.34749, 171.662
14generate(-0.88161, -0.37695, -0.28401), (-0.38033, 0.21109, 0.90044), (-0.27947, 0.90186, -0.32947)-240.43364, -31.51826, -58.03983
15generate(0.76808, -0.57456, -0.28272), (0.00854, -0.43228, 0.9017), (-0.64029, -0.69499, -0.32712)28.95652, 84.59862, 28.00809
16generate(-0.10345, -0.32264, -0.94085), (-0.89785, 0.43732, -0.05125), (0.42799, 0.83944, -0.33492)-95.1169, -85.33239, 55.52859
17generate(0.26798, -0.28026, 0.92176), (-0.28524, -0.93694, -0.20195), (0.92023, -0.2088, -0.33102)21.55405, 48.95417, -42.34116
18generate(-0.9872, 0.14948, -0.05564), (0.14842, 0.7332, -0.66362), (-0.0584, -0.66339, -0.746)-161.33823, -10.31573, -131.76878
19generate(-0.35132, 0.93626, -0.00045), (0.93626, 0.35132, 3.0E-5), (0.00019, -0.00041, -1)-136.2807, 111.90674, -169.20938
20generate(0.17659, -0.81786, -0.54764), (-0.81648, -0.43245, 0.38255), (-0.5497, 0.37959, -0.74414)-27.21439, -16.58027, -33.39512

-
Components

#1: Protein Capsid protein / Capsid


Mass: 29741.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triatoma virus / References: UniProt: Q9QEY5
#2: Protein Capsid protein / Capsid


Mass: 28519.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triatoma virus / References: UniProt: Q9QEY5
#3: Protein Capsid protein / Capsid


Mass: 31933.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triatoma virus / References: UniProt: Q9QEY5

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystal were growth at 291.15 K by vapor diffusion in sitting drop plates mixing equal volumes of the capsid solution at 3 mg/mL and of the reservoir solution: 100 mM Tris pH 8.5, 50 mM ...Details: Crystal were growth at 291.15 K by vapor diffusion in sitting drop plates mixing equal volumes of the capsid solution at 3 mg/mL and of the reservoir solution: 100 mM Tris pH 8.5, 50 mM MgCl2 and 25% pentaerythritol propoxilate 629.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.6→49.91 Å / Num. obs: 315756 / % possible obs: 98 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 5.17
Reflection shellResolution: 3.6→3.7 Å / Redundancy: 2.2 % / % possible all: 97

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NAP

3nap


Resolution: 3.6→49.91 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.861 / SU B: 55.14 / SU ML: 0.693 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26917 6432 2 %RANDOM
Rwork0.26873 ---
obs0.26874 309319 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 113.221 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----1.76 Å2
Refinement stepCycle: 1 / Resolution: 3.6→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 0 0 5398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.025549
X-RAY DIFFRACTIONr_bond_other_d0.0010.025210
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9597585
X-RAY DIFFRACTIONr_angle_other_deg0.719312002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3955682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02823.814236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61315857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9531525
X-RAY DIFFRACTIONr_chiral_restr0.0620.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021279
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.85811.0052737
X-RAY DIFFRACTIONr_mcbond_other3.85811.0042736
X-RAY DIFFRACTIONr_mcangle_it6.33316.4973416
X-RAY DIFFRACTIONr_mcangle_other6.33216.4993417
X-RAY DIFFRACTIONr_scbond_it4.50611.7322812
X-RAY DIFFRACTIONr_scbond_other4.50511.7332813
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.87517.3494169
X-RAY DIFFRACTIONr_long_range_B_refined11.04891.146599
X-RAY DIFFRACTIONr_long_range_B_other11.04791.156600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded

+
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