|Entry||Database: PDB / ID: 2x8q|
|Title||Cryo-EM 3D model of the icosahedral particle composed of Rous sarcoma virus capsid protein pentamers|
|Components||CAPSID PROTEIN P27|
|Keywords||VIRUS / CAPSID PROTEIN / VIRAL MATRIX PROTEIN|
|Function / homology|
Function and homology information
host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / structural constituent of virion / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / nucleic acid binding / aspartic-type endopeptidase activity / zinc ion binding
gag protein p24 N-terminal domain / Retroviral Gag polyprotein, M / Zinc finger, CCHC-type superfamily / Retropepsin-like catalytic domain / Aspartic peptidase domain superfamily / Retropepsins / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Retrovirus capsid, C-terminal ...gag protein p24 N-terminal domain / Retroviral Gag polyprotein, M / Zinc finger, CCHC-type superfamily / Retropepsin-like catalytic domain / Aspartic peptidase domain superfamily / Retropepsins / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Retrovirus capsid, C-terminal / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Zinc finger, CCHC-type / Retroviral nucleocapsid protein Gag, p24 fragment
|Biological species||ROUS SARCOMA VIRUS - PRAGUE C|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 18.3 Å|
|Model type details||CA ATOMS ONLY, CHAIN A|
|Authors||K Hyun, J. / Radjainia, M. / Kingston, R.L. / Mitra, A.K.|
|Citation||Journal: J Biol Chem / Year: 2010|
Title: Proton-driven assembly of the Rous Sarcoma virus capsid protein results in the formation of icosahedral particles.
Authors: Jae-Kyung Hyun / Mazdak Radjainia / Richard L Kingston / Alok K Mitra /
Abstract: In a mature and infectious retroviral particle, the capsid protein (CA) forms a shell surrounding the genomic RNA and the replicative machinery of the virus. The irregular nature of this capsid shell ...In a mature and infectious retroviral particle, the capsid protein (CA) forms a shell surrounding the genomic RNA and the replicative machinery of the virus. The irregular nature of this capsid shell precludes direct atomic resolution structural analysis. CA hexamers and pentamers are the fundamental building blocks of the capsid, however the pentameric state, in particular, remains poorly characterized. We have developed an efficient in vitro protocol for studying the assembly of Rous sarcoma virus (RSV) CA that involves mild acidification and produces structures modeling the authentic viral capsid. These structures include regular spherical particles with T = 1 icosahedral symmetry, built from CA pentamers alone. These particles were subject to cryoelectron microscopy (cryo-EM) and image processing, and a pseudo-atomic model of the icosahedron was created by docking atomic structures of the constituent CA domains into the cryo-EM-derived three-dimensional density map. The N-terminal domain (NTD) of CA forms pentameric turrets, which decorate the surface of the icosahedron, while the C-terminal domain (CTD) of CA is positioned underneath, linking the pentamers. Biophysical analysis of the icosahedral particle preparation reveals that CA monomers and icosahedra are the only detectable species and that these exist in reversible equilibrium at pH 5. These same acidic conditions are known to promote formation of a RSV CA CTD dimer, present within the icosahedral particle, which facilitates capsid assembly. The results are consistent with a model in which RSV CA assembly is a nucleation-limited process driven by very weak protein-protein interactions.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: CAPSID PROTEIN P27
A: CAPSID PROTEIN P27x 60
A: CAPSID PROTEIN P27x 5
A: CAPSID PROTEIN P27x 6
|Symmetry||Point symmetry: (Schoenflies symbol: I (icosahedral))|
|#1: Protein|| |
Mass: 24472.230 Da / Num. of mol.: 1 / Fragment: RESIDUES 240-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ROUS SARCOMA VIRUS - PRAGUE C
Description: RECOMBINANT ROUS SARCOMA VIRUS CAPSID PROTEIN WAS PRODUCED BY HETEROLOGOUS EXPRESSION IN E. COLI AND PURIFIED TO HOMOGENIETY
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 / References: UniProt: P03322
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: ICOSAHEDRAL PARTICLES COMPOSED OF ROUS SARCOMA VIRUS CAPSID PROTEIN|
|Buffer solution||Name: 0.1M CITRIC ACID, 5MM MOPS/KOH, 725MM NACL, 0.25MM NA AZIDE, 0.125MM TCEP-HCL|
Details: 0.1M CITRIC ACID, 5MM MOPS/KOH, 725MM NACL, 0.25MM NA AZIDE, 0.125MM TCEP-HCL
|Specimen||Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: HOLEY CARBON|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE|
Details: CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 85, INSTRUMENT- VITROBOT MARK IV, METHOD- BLOT FOR 5 SECONDS BEFORE PLUNGING,
-Electron microscopy imaging
|Microscopy||Model: FEI TECNAI 12|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 42000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2 mm|
|Specimen holder||Temperature: 103 K|
|Image recording||Electron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM|
|Image scans||Num. digital images: 21|
|Radiation wavelength||Relative weight: 1|
|CTF correction||Details: EACH MICROGRAPH|
|Symmetry||Point symmetry: I (icosahedral)|
|3D reconstruction||Method: POLAR FOURIER TRANSFORM / Resolution: 18.3 Å / Num. of particles: 1310 / Nominal pixel size: 2.5 Å / Actual pixel size: 2.5 Å|
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1710.
Symmetry type: POINT
|Atomic model building||Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY|
|Atomic model building|
|Refinement||Highest resolution: 18.3 Å|
|Refinement step||Cycle: LAST / Highest resolution: 18.3 Å|
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+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. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+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. See below links for details.
- 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.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
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.
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