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- EMDB-1547: Structure of GroEL in complex with non-native capsid protein gp23... -

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Basic information

Entry
Database: EMDB / ID: 1547
TitleStructure of GroEL in complex with non-native capsid protein gp23, Bacteriophage T4 co-chaperone gp31 and ADPAlF3
Keywordschaperonin / bacteriophage T4 / capsid protein gp23 / GroEL / co-chaperone gp31
SampleGroEL-gp31-gp23(1)-ADPALF3
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Enterobacteria phage T4 / virus / Bacteriophage T4
Synthetic construct
Map dataVolume contains GroEL in complex with non-native capsid protein gp23, co-chaperonin gp31 and ADPAlF3
Methodsingle particle reconstruction, at 10.2 A resolution
AuthorsClare DK / Bakkes PJ / van Heerikhuizen H / van der Vies SM / Saibil HR
CitationNature, 2009, 457, 107-110

Nature, 2009, 457, 107-110 StrPapers
Chaperonin complex with a newly folded protein encapsulated in the folding chamber.
D K Clare / P J Bakkes / H van Heerikhuizen / S M van der Vies / H R Saibil

DateDeposition: Sep 2, 2008 / Header (metadata) release: Sep 3, 2008 / Map release: Apr 2, 2009 / Last update: Sep 2, 2008

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.15
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-2cgt
  • Surface level: 0.15
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_1547.map.gz (map file in CCP4 format, 16001 KB)
Projections & slicesSize of images:
AxesZ (Sec.)X (Row.)Y (Col.)
160 pix
2.8 A/pix
= 448. A
160 pix
2.8 A/pix
= 448. A
160 pix
2.8 A/pix
= 448. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.8 A
Density
Contour Level:0.0947, 0.15 (movie #1):
Minimum - Maximum-1.94969 - 3.39623
Average (Standard dev.)0.00648203 (0.0950591)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions160160160
Origin-81-81-81
Limit787878
Spacing160160160
CellA=B=C: 448 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.82.82.8
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z448.000448.000448.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S213
start NC/NR/NS-81-81-81
NC/NR/NS160160160
D min/max/mean-1.9503.3960.006

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Supplemental data

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Sample components

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Entire GroEL-gp31-gp23(1)-ADPALF3

EntireName: GroEL-gp31-gp23(1)-ADPALF3
Details: one copy of gp23 is bound to GroEL in the opposite ring to that of the co-chaperonin gp31
Number of components: 4
Oligomeric State: tetradecamer of GroEL bound to a heptamer of gp31 and a monomer of gp23
MassTheoretical: 950 kDa / Experimental: 950 kDa / Measured by: sequence

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Component #1: protein, GroEL

ProteinName: GroEL / a.k.a: GroEL / Oligomeric Details: tetradecamer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 56 kDa / Experimental: 56 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: MC1009
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pSL6
Source (natural)Location in cell: Cytoplasm
External referencesGene Ontology: GO: 0005515 / InterPro: InterPro: 001844

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Component #2: protein, gp31

ProteinName: gp31 / a.k.a: bacteriophage T4 co-chaperonin / Oligomeric Details: heptamer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 12 kDa / Experimental: 12 kDa
SourceSpecies: Enterobacteria phage T4 / virus / Bacteriophage T4
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pAR1
Source (natural)Location in cell: Cytoplasm
External referencesInterPro: InterPro: 016416

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Component #3: protein, gp23

ProteinName: gp23 / a.k.a: Major capsid protein / Oligomeric Details: monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 56 kDa / Experimental: 56 kDa
SourceSpecies: Enterobacteria phage T4 / virus / Bacteriophage T4
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pET2331
Source (natural)Location in cell: Cytoplasm
External referencesInterPro: InterPro: 010762

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Component #4: ligand, ADPAlF3

LigandName: ADPAlF3 / a.k.a: Non-hydrolysable ATP analogue / Oligomeric Details: monomer / Recombinant expression: No / Number of Copies: 14
SourceSpecies: Synthetic construct

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 40 mM Tris-HCl pH 7.5, 10 mM KCl, 10 mM MgCl2, 2.5 mM ADPAlF3 After nucleotide addition the sample was incubated for 15 minutes before vitrification
pH: 7.5
Support film400 mesh R2/2 c-flat grids
StainingCryo
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 100 K / Method: blot for 2-3 seconds before plunging / Details: Vitrification instrument: manual plunger

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Jun 1, 2006
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: corrected at 150,00 times / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm
Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN / Temperature: 100 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 150 / Scanner: ZEISS SCAI / Sampling size: 1.4 microns / Bit depth: 8 / OD range: 0.5

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 7300 / Details: No symmetry was applied / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: SIRT
Euler angles: SPIDER:theta 90-110 degrees, phi 0-360 degrees. Mirror option was on.
Software: SPIDER / CTF correction: Each particle / Details: No symmetry was applied to the reconstruction / Resolution: 10.2 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: URO / Refinement protocol: rigid body / Target criteria: cross-correlation coefficient / Refinement space: RECIPROCAL
Details: Protocol: Individual domains fitted as rigid bodies. The domains were separately fitted in URO
Input PDB model: 2CGT
Output model

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