[English] 日本語
Yorodumi
- PDB-3g21: Crystal structure of the C-terminal domain of the Rous Sarcoma Vi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g21
TitleCrystal structure of the C-terminal domain of the Rous Sarcoma Virus capsid protein: Low pH
ComponentsGag polyproteinGroup-specific antigen
KeywordsVIRAL PROTEIN / ALPHA-HELICAL BUNDLE / CAPSID PROTEIN / VIRION / RETROVIRUS
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
Retroviral Gag polyprotein, M / Zinc finger, CCHC-type / Retroviral matrix protein / Retrovirus capsid, N-terminal / Retrovirus capsid, C-terminal / Aspartic peptidase domain superfamily / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Retroviral nucleocapsid protein Gag, p24 fragment / Retropepsins ...Retroviral Gag polyprotein, M / Zinc finger, CCHC-type / Retroviral matrix protein / Retrovirus capsid, N-terminal / Retrovirus capsid, C-terminal / Aspartic peptidase domain superfamily / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Retroviral nucleocapsid protein Gag, p24 fragment / Retropepsins / Retropepsin-like catalytic domain / Zinc finger, CCHC-type superfamily / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Gag polyprotein
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsKingston, R.L.
CitationJournal: Structure / Year: 2009
Title: Proton-linked dimerization of a retroviral capsid protein initiates capsid assembly
Authors: Bailey, G.D. / Hyun, J.K. / Mitra, A.K. / Kingston, R.L.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5372
Polymers8,4751
Non-polymers621
Water1,49583
1
A: Gag polyprotein
hetero molecules

A: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0734
Polymers16,9492
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1480 Å2
ΔGint-2 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)32.179, 32.179, 113.875
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Gag polyprotein / Group-specific antigen / Capsid protein


Mass: 8474.636 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 389-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Strain: Prague C Strain / Gene: gag / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: P03322, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: 0.20M Succinic acid/KOH, pH4.3, 13-18% PEG8000, 0.75M Magnesium Nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.85503 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 28, 2008
RadiationMonochromator: Double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85503 Å / Relative weight: 1
ReflectionResolution: 0.9→27 Å / Num. all: 46299 / Num. obs: 46299 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 36.2
Reflection shellResolution: 0.9→0.93 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 7.2 / Num. unique all: 1546 / % possible all: 30

-
Processing

Software
NameClassification
Blu-Icedata collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G1G
Resolution: 0.9→27 Å / Num. parameters: 7348 / Num. restraintsaints: 10719
Isotropic thermal model: Restrained Anisotropic Thermal Parameters
Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.142 2306 -RANDOM
Rwork0.124 ---
Obs0.124 43916 84.6 %-
All-43916 --
Solvent computationSolvent model: Moews and Kretsinger (Babinet scaling)
Refine analyzeNum. disordered residues: 42 / Occupancy sum hydrogen: 583.31 / Occupancy sum non hydrogen: 669.09
Refinement stepCycle: LAST / Resolution: 0.9→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 4 101 812
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0252
X-RAY DIFFRACTIONs_zero_chiral_vol0.114
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.112
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.164
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0.078

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (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

External links:EMDB at PDBe / 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. 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.

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

+
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

Read more

-
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.

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