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

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1547
Title	Structure of GroEL in complex with non-native capsid protein gp23, Bacteriophage T4 co-chaperone gp31 and ADPAlF3
Map	Volume contains GroEL in complex with non-native capsid protein gp23, co-chaperonin gp31 and ADPAlF3
Sample	GroEL-gp31-gp23(1)-ADPALF3
Keywords	chaperonin, bacteriophage T4, capsid protein gp23, GroEL, co-chaperone gp31
Authors	Clare DK, Bakkes PJ, van Heerikhuizen H, van der Vies SM, Saibil HR
Date	Deposition: 2008-09-02, Header release: 2008-09-03, Map release: 2009-04-02, Last update: 2012-10-24
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.15, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.15, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-2cgt, Surface level: 0.15, Made by UCSF CHIMERA
Supplemental images	1547.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-2cgt Fit EMDB-1544 Cite EMDB-1545 Cite EMDB-1546 Cite EMDB-1548 Cite Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-1546 EMDB-1548 EMDB-1202 EMDB-1588 EMDB-1203 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Nature, Vol. 457, Issue 7225, Page 107-10, Year 2009
Title	Chaperonin complex with a newly folded protein encapsulated in the folding chamber.
Authors	D K Clare, P J Bakkes, H van Heerikhuizen, S M van der Vies, H R Saibil Department of Crystallography and Institute for Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK.
Keywords	Capsid Proteins (chemistry), Chaperonin 10 (chemistry), Chaperonin 60 (chemistry), Models, Molecular, Multiprotein Complexes (chemistry), Protein Folding, Viral Proteins (chemistry), gene 31 protein, Enterobacteria phage T4, gp23 protein, Bacteriophage T4
Links	DOI: 10.1038/nature07479, PubMed: 19122642, PMC: PMC2728927

Map

File

EMD-1547.map ( map file in CCP4 format, 16386 KB )

Projections & Slices

Size of images:

Axes	Z (Sec.)	X (Row.)	Y (Col.)
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)

Contour Level:	0.0947, 0.15 (movie #1):
Minimum - Maximum:	-1.94969 - 3.39623
Average (Standard dev.):	0.00648203 (0.0950591)

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Axis Order :	Y	X	Z
Dimensions :	160	160	160
Origin :	-81	-81	-81
Limit :	78	78	78
Spacing :	160	160	160

Unit Cell

A = 448 A , B = 448 A , C = 448 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 2.8 A , Y = 2.8 A , Z = 2.8 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.8	2.8	2.8
M x/y/z	160	160	160
origin x/y/z	0.000	0.000	0.000
length x/y/z	448.000	448.000	448.000
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-81	-81	-81
NX/NY/NZ	160	160	160
MAP C/R/S	2	1	3
start NC/NR/NS	-81	-81	-81
NC/NR/NS	160	160	160
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-1.950	3.396	0.006

Annotation Details

Volume contains GroEL in complex with non-native capsid protein gp23, co-chaperonin gp31 and ADPAlF3

Supplement
Images
Images	1547.gif

Sample
Name	GroEL-gp31-gp23(1)-ADPALF3
Number of Components	4
Oligomeric State	tetradecamer of GroEL bound to a heptamer of gp31 and a monomer of gp23
Theoretical Mass	0.95 MDa
Details	one copy of gp23 is bound to GroEL in the opposite ring to that of the co-chaperonin gp31
Mass-estimation Method	sequence
Experimental Mass	0.95 MDa
Component #1: protein - GroEL
Scientific name	GroEL
Theoretical Mass	0.056 MDa
Experimental Mass	0.056 MDa
Oligomeric Details	tetradecamer
Number of Copies	1
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Strain	MC1009
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Vector: pSL6 Exp System: Escherichia coli (NCBI Taxonomy: 562)
Links	Gene Ontology: GO:0005515, InterPro: IPR:001844
Component #2: protein - bacteriophage T4 co-chaperonin
Scientific name	gp31
Common Name	bacteriophage T4 co-chaperonin
Theoretical Mass	0.012 MDa
Experimental Mass	0.012 MDa
Oligomeric Details	heptamer
Number of Copies	1
Scientific Name of Species	Enterobacteria phage T4 (NCBI Taxonomy: 10665)
Common Name of Species	Bacteriophage T4
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562) Vector: pAR1
Links	InterPro: IPR:016416
Component #3: protein - Major capsid protein
Scientific name	gp23
Common Name	Major capsid protein
Theoretical Mass	0.056 MDa
Experimental Mass	0.056 MDa
Oligomeric Details	monomer
Number of Copies	1
Scientific Name of Species	Enterobacteria phage T4 (NCBI Taxonomy: 10665)
Common Name of Species	Bacteriophage T4
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Vector: pET2331 Exp System: Escherichia coli (NCBI Taxonomy: 562)
Links	InterPro: IPR:010762
Component #4: ligand - Non-hydrolysable ATP analogue
Scientific name	ADPAlF3
Common Name	Non-hydrolysable ATP analogue
Oligomeric Details	monomer
Number of Copies	14
Scientific Name of Species	synthetic construct (NCBI Taxonomy: 32630)
Recombinant expression	No

Experiment
Sample Preparation
Staining	Cryo
Specimen Conc	1 mg/ml
Specimen Support Details	400 mesh R2/2 c-flat grids
Specimen State	particle
Buffer	Details: 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
Vitrification
Method	blot for 2-3 seconds before plunging
Cryogen Name	ETHANE
Details	Vitrification instrument: manual plunger
Instrument	HOMEMADE PLUNGER
Temperature	100 Kelvin
Imaging
Microscope	FEI TECNAI F20
Date	01-JUN-2006
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	15 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X, Calibrated: 50000 X
Astigmatism	corrected at 150,00 times
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	1000 nm - 3000 nm
Specimen Holder
Holder	side entry ( GATAN LIQUID NITROGEN )
Temperature	100 Kelvin
Camera
Detector	Kodak SO163
Image Acquisition
Od Range	0.5
Scanner	ZEISS SCAI
Number of Digital Images	150
Sampling Size	1.4 microns
Quant Bit Number	8

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	SIRT
Euler Angles Details	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 By Author	10.2
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	7300
Details	No symmetry was applied
Atomic Model Fitting
Model #0
Target Criteria	cross-correlation coefficient
Details	Protocol: Individual domains fitted as rigid bodies. The domains were separately fitted in URO
Software	URO
Refinement Protocol	rigid body
Refinement Space	RECIPROCAL
Fitted Coordinate
PDB entry ID	PDB-2cgt

Download

Data from EMDB

Header (meta data in XML format)

emd-1547.xml (11.6 KB)

Map data

emd_1547.map.gz (229 KB)

Images

1547.gif (42.9 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1547

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5.4 MB Session file for UCSF-Chimera, 19.7 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.3 MB .webm (WebM/VP8 format), 5 MB Session file for UCSF-Chimera, 19.8 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.8 MB .webm (WebM/VP8 format), 5.3 MB Session file for UCSF-Chimera, 6.1 MB