[English] 日本語
Yorodumi
- PDB-1fou: CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fou
TitleCONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29
ComponentsUPPER COLLAR PROTEIN
KeywordsVIRAL PROTEIN / alpha-helical barrel
Function / homology
Function and homology information


viral portal complex / viral procapsid / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / RNA binding
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #30 / Upper collar protein gp10 (connector protein) fold / Upper collar protein gp10 (connector protein) / Bacteriophage PHI-29 conector. Domain 3 / Portal protein Gp10 / Portal protein Gp10 superfamily / Phage Connector (GP10) / Crambin / Serum Albumin; Chain A, Domain 1 / Beta Barrel ...Serum Albumin; Chain A, Domain 1 - #30 / Upper collar protein gp10 (connector protein) fold / Upper collar protein gp10 (connector protein) / Bacteriophage PHI-29 conector. Domain 3 / Portal protein Gp10 / Portal protein Gp10 superfamily / Phage Connector (GP10) / Crambin / Serum Albumin; Chain A, Domain 1 / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsSimpson, A.A. / Tao, Y. / Leiman, P.G. / Badasso, M.O. / He, Y. / Jardine, P.J. / Olson, N.H. / Morais, M.C. / Grimes, S.N. / Anderson, D.L. ...Simpson, A.A. / Tao, Y. / Leiman, P.G. / Badasso, M.O. / He, Y. / Jardine, P.J. / Olson, N.H. / Morais, M.C. / Grimes, S.N. / Anderson, D.L. / Baker, T.S. / Rossmann, M.G.
CitationJournal: Nature / Year: 2000
Title: Structure of the bacteriophage phi29 DNA packaging motor.
Authors: A A Simpson / Y Tao / P G Leiman / M O Badasso / Y He / P J Jardine / N H Olson / M C Morais / S Grimes / D L Anderson / T S Baker / M G Rossmann /
Abstract: Motors generating mechanical force, powered by the hydrolysis of ATP, translocate double-stranded DNA into preformed capsids (proheads) of bacterial viruses and certain animal viruses. Here we ...Motors generating mechanical force, powered by the hydrolysis of ATP, translocate double-stranded DNA into preformed capsids (proheads) of bacterial viruses and certain animal viruses. Here we describe the motor that packages the double-stranded DNA of the Bacillus subtilis bacteriophage phi29 into a precursor capsid. We determined the structure of the head-tail connector--the central component of the phi29 DNA packaging motor--to 3.2 A resolution by means of X-ray crystallography. We then fitted the connector into the electron densities of the prohead and of the partially packaged prohead as determined using cryo-electron microscopy and image reconstruction analysis. Our results suggest that the prohead plus dodecameric connector, prohead RNA, viral ATPase and DNA comprise a rotary motor with the head-prohead RNA-ATPase complex acting as a stator, the DNA acting as a spindle, and the connector as a ball-race. The helical nature of the DNA converts the rotary action of the connector into translation of the DNA.
History
DepositionAug 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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: UPPER COLLAR PROTEIN
B: UPPER COLLAR PROTEIN
C: UPPER COLLAR PROTEIN
D: UPPER COLLAR PROTEIN
E: UPPER COLLAR PROTEIN
F: UPPER COLLAR PROTEIN
G: UPPER COLLAR PROTEIN
H: UPPER COLLAR PROTEIN
I: UPPER COLLAR PROTEIN
J: UPPER COLLAR PROTEIN
K: UPPER COLLAR PROTEIN
L: UPPER COLLAR PROTEIN


Theoretical massNumber of molelcules
Total (without water)431,54712
Polymers431,54712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72370 Å2
ΔGint-354 kcal/mol
Surface area124490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.16, 169.24, 185.44
Angle α, β, γ (deg.)90, 114.1, 90
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Detailsthe biological entity is the same dodecamer found in the crystal assymetric unit

-
Components

#1: Protein
UPPER COLLAR PROTEIN / GP 10 / CONNECTOR PROTEIN / LATE PROTEIN GP10 / P10 CONNECTOR PROTEIN


Mass: 35962.289 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Plasmid: PPC28D1 / Production host: Bacillus subtilis (bacteria) / References: UniProt: P04332

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30 % MPD, 0.05 M CaCl2, 0.1M Tris HCL, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion / Details: Badasso, M.O., (2000) Acta Crystallogr. D56, 1187.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-10 mg/mlprotein1drop
25 mMTris-HCl1drop
30.4 M1dropNaCl
40.1 MHEPES1drop
50.2 M1dropMgCl2
60.2 MMPD1reservoir
70.1 MHEPES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.21→9 Å / Num. all: 78465 / Num. obs: 78035 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 21
Reflection shellResolution: 3.21→3.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.198 / Num. unique all: 2043 / % possible all: 100
Reflection
*PLUS
Highest resolution: 3.2 Å / Rmerge(I) obs: 0.065
Reflection shell
*PLUS

-
Processing

Software
NameClassification
AMoREphasing
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementResolution: 3.2→9 Å / Cross valid method: THROUGHOUT / σ(F): 5 / Stereochemistry target values: Engh & Huber / Details: restrained least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.36 3898 5 %random
Rwork0.29 ---
all0.27 78465 --
obs0.27 78035 99.5 %-
Refinement stepCycle: LAST / Resolution: 3.2→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25272 0 0 0 25272
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_bond_d0.009
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 9 Å / σ(F): 5 / % reflection Rfree: 5 % / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.6

+
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