[English] 日本語
Yorodumi
- PDB-4il7: Crystal structure of A223 C-terminal domain, a structural protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4il7
TitleCrystal structure of A223 C-terminal domain, a structural protein from sulfolobus turreted icosahedral virus (STIV)
ComponentsPutative uncharacterized protein
KeywordsVIRAL PROTEIN / partial jelly roll fold / hypothetical protein / C381 and B345 / Viral Capsid
Function / homologyJelly Rolls - #1300 / : / A223 penton protein second domain / Jelly Rolls / Sandwich / Mainly Beta / A223 penton protein C-terminal domain-containing protein
Function and homology information
Biological speciesSulfolobus turreted icosahedral virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsSendamarai, A.K. / Lawrence, C.M.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Atomic structure of the 75 MDa extremophile Sulfolobus turreted icosahedral virus determined by CryoEM and X-ray crystallography.
Authors: David Veesler / Thiam-Seng Ng / Anoop K Sendamarai / Brian J Eilers / C Martin Lawrence / Shee-Mei Lok / Mark J Young / John E Johnson / Chi-yu Fu /
Abstract: Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution ...Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution electron microscopy and X-ray crystallography allowing tracing of structural polypeptide chains and visualization of transmembrane proteins embedded in the viral membrane. We propose that the vertex complexes orchestrate virion assembly by coordinating interactions of the membrane and various protein components involved. STIV shares the same coat subunit and penton base protein folds as some eukaryotic and bacterial viruses, suggesting that they derive from a common ancestor predating the divergence of the three kingdoms of life. One architectural motif (β-jelly roll fold) forms virtually the entire capsid (distributed in three different gene products), indicating that a single ancestral protein module may have been at the origin of its evolution.
History
DepositionDec 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,9351
Polymers17,9351
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.853, 65.853, 43.673
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Putative uncharacterized protein / Hypothetical protein A223


Mass: 17935.160 Da / Num. of mol.: 1 / Mutation: L208M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus turreted icosahedral virus / Gene: A223 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6Q0L4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.52 Å3/Da / Density % sol: 19.3 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 10-15%v/v 2-Propanol, 5-10%w/v Polyethylene glycol 4,000, 0.1M Sodium citrate tribasic dihydrate 5.6 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95369
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2010
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 21677 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rsym value: 0.028 / Net I/σ(I): 23
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 5.2 % / Rsym value: 0.255 / % possible all: 89.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→19.34 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.711 / SU ML: 0.031 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16506 1021 5 %RANDOM
Rwork0.14017 ---
obs0.14136 19450 93.56 %-
all-21677 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.117 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.47 Å20 Å2
2---0.47 Å20 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms631 0 0 102 733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02759
X-RAY DIFFRACTIONr_bond_other_d0.0010.02700
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.9521058
X-RAY DIFFRACTIONr_angle_other_deg1.75831628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.4927.14328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59715126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02934
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02170
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr3.78531459
X-RAY DIFFRACTIONr_sphericity_free36.541530
X-RAY DIFFRACTIONr_sphericity_bonded9.65551507
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 91 -
Rwork0.178 1523 -
obs--99.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.798-0.7077-0.802811.0876-4.91175.4353-0.12570.0599-0.5305-0.1494-0.01560.23310.2843-0.18220.14130.05520.0070.03320.0758-0.03330.08586.627419.5991-0.5892
21.70961.4212-0.07397.70420.69371.15490.07130.08770.0796-0.0619-0.11-0.18730.067-0.02980.03870.06980.01590.00390.08560.01550.02668.77832.5873-1.9725
33.20164.122-0.43768.4159-2.11352.2023-0.54020.4867-0.5112-0.52840.1746-0.3792-0.0742-0.27740.36560.1805-0.02250.07690.321-0.23620.2775-0.459323.4309-3.3029
49.07326.0315-0.03887.8952-1.12871.6397-0.0633-0.4977-0.52140.2256-0.02790.14950.1014-0.01870.09120.07940.02250.06830.1030.05240.14772.639420.34588.0066
58.66545.13863.83493.07772.28851.70490.1322-0.14090.16160.1383-0.11690.00120.0842-0.066-0.01520.140.0202-0.07860.194-0.02830.30814.461834.58839.1997
65.6072-1.11261.99381.70740.2263.8109-0.0901-0.18110.27330.14580.0139-0.0041-0.0457-0.00070.07610.0757-0.0090.01610.1171-0.01630.04113.680135.43119.4533
712.7782.73920.04110.8016-0.5141.2984-0.17940.1942-0.209-0.08860.1157-0.05310.1011-0.12430.06360.0942-0.0245-0.00170.1427-0.01560.1316-9.4826.12433.4467
811.11773.36536.86052.18072.32734.29080.1373-0.0674-0.1560.0176-0.0740.06550.0795-0.0712-0.06330.0719-0.01670.02030.1107-0.00480.068-7.634729.21428.0838
910.5096-2.52470.30220.95780.82763.658-0.1717-0.368-0.18810.25090.15580.03870.25950.30170.01590.18310.0182-0.01240.1291-0.00660.05146.865630.871112.0472
107.41942.06723.13434.09631.72353.864-0.0072-0.5252-0.52880.172-0.11940.18640.1388-0.23950.12670.0530.00370.06360.11260.01960.1477-2.120620.99857.9454
1110.79374.27450.21559.965-1.52532.6537-0.18360.3350.0286-0.23640.10060.3311-0.0041-0.15380.0830.0350.01260.00190.0807-0.01580.0278-2.533829.44910.1722
123.9238-1.40020.31993.58640.36092.98770.0504-0.24150.34310.0805-0.0283-0.1556-0.16580.033-0.0220.0434-0.0021-0.00470.0662-0.00130.04818.69837.39353.8037
134.7072.0259-0.71265.93-0.33531.5006-0.1831-0.2323-0.37830.2094-0.01120.06310.05980.00680.19430.03940.02310.03880.0648-0.00070.0756.911721.61094.1949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A139 - 143
2X-RAY DIFFRACTION2A144 - 150
3X-RAY DIFFRACTION3A151 - 158
4X-RAY DIFFRACTION4A159 - 165
5X-RAY DIFFRACTION5A166 - 171
6X-RAY DIFFRACTION6A172 - 177
7X-RAY DIFFRACTION7A178 - 183
8X-RAY DIFFRACTION8A184 - 188
9X-RAY DIFFRACTION9A189 - 194
10X-RAY DIFFRACTION10A195 - 203
11X-RAY DIFFRACTION11A204 - 208
12X-RAY DIFFRACTION12A209 - 215
13X-RAY DIFFRACTION13A216 - 221

+
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