PDB-4aaq: ATP-triggered molecular mechanics of the chaperonin GroEL

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 4aaq
Title	ATP-triggered molecular mechanics of the chaperonin GroEL
Descriptor	60 KDA CHAPERONIN
Keywords	CHAPERONE
Authors	Clare, D.K., Vasishtan, D., Stagg, S., Quispe, J., Farr, G.W., Topf, M., Horwich, A.L., Saibil, H.R.
Date	Deposition: 2011-12-05, Release: 2012-12-12
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Compound details	ENGINEERED RESIDUE IN CHAIN A, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN C, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN D, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN E, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN F, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN G, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN H, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN I, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN J, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN K, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN L, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN M, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN N, ASP 398 TO ALA
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1998, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1998 CiteFit EMDB-1997 Cite EMDB-1999 Cite EMDB-2000 Cite EMDB-2001 Cite EMDB-2002 Cite EMDB-2003 Cite PDB-4aar Cite PDB-4aas Cite PDB-4aau Cite PDB-4ab2 Cite PDB-4ab3 Cite PDB-1aon PDB-1dk7 PDB-1dkd PDB-1fy9 PDB-1fya PDB-1gr5 PDB-1grl PDB-1gru PDB-1j4z PDB-1jon PDB-1kid PDB-1kp8 PDB-1kpo PDB-1la1 PDB-1mnf PDB-1oel PDB-1pcq PDB-1pf9 PDB-1ss8 PDB-1svt PDB-1sx3 PDB-1sx4 PDB-1xck PDB-2c7c PDB-2c7d PDB-2c7e PDB-2cgt PDB-2yey Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-4aar EMDB-5002 EMDB-5143 EMDB-1998 PDB-2ynj PDB-1gr5 List of similar structure data about Omokage system

Article
Citation - primary
Article	Cell, Vol. 149, Issue 1, Page 113-23, Year 2012
Title	ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin.
Authors	Daniel K Clare, Daven Vasishtan, Scott Stagg, Joel Quispe, George W Farr, Maya Topf, Arthur L Horwich, Helen R Saibil Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK.
Keywords	Adenosine Triphosphate (metabolism, 56-65-5), Bacteria (chemistry), Chaperonin 10 (metabolism), Chaperonin 60 (chemistry), Cryoelectron Microscopy, Escherichia coli (chemistry), Escherichia coli Proteins (chemistry), GroE protein, E coli, Heat-Shock Proteins (chemistry), Hydrophobic and Hydrophilic Interactions, Protein Conformation, Protein Folding
Links	PII: S0092-8674(12)00287-5, DOI: 10.1016/j.cell.2012.02.047, PubMed: 22445172, PMC: PMC3326522

Components
ID 1 : HSP60, GROEL PROTEIN, PROTEIN CPN60
Image
Description	60 KDA CHAPERONIN
Type	polymer
Mutation	YES
Formula weight	57348.242 Da
Number of molecules	14
Details	ATPASE MUTANT, ATP BOUND IN ONE RING. CHAINS A-G ARE IN THE RS1 ATP BOUND CONFORMATION CHAINS H-N ARE IN THE APO CONFORMATION.
Source	Method: Isolated from a genetically manipulated source Gene: ID:562, ESCHERICHIA COLI Host: ID:562, ESCHERICHIA COLI
Links	UniProt: P0A6F5, Sequence view
ID 2 : ADENOSINE-5'-TRIPHOSPHATE
Image
Description	ADENOSINE-5'-TRIPHOSPHATE
Type	non-polymer
Formula weight	507.183 Da
Number of molecules	7
Source	Method: Obtained synthetically
ID 3 : PHOSPHATE ION
Image
Description	PHOSPHATE ION
Type	non-polymer
Formula weight	94.971 Da
Number of molecules	7
Source	Method: Obtained synthetically
ID 4 : MAGNESIUM ION
Image
Description	MAGNESIUM ION
Type	non-polymer
Formula weight	24.305 Da
Number of molecules	7
Source	Method: Obtained synthetically

Sample
Assembly
Aggregation state	PARTICLE
Name	GROEL-ATP7 RS1
Buffer
Name	50 MM TRIS-HCL PH 7.4, 50 MM KCL, 10 MM MGCL2 AND 200UM ATP
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	CRYO EM
Sample preparation
pH	7.4
Sample concentration	4.0 mg/ml
Sample support
Details	HOLEY CARBON
Vitrification
Details	VITRIFIED WITH A VITROBOT AT 100 PERCENT HUMIDITY WITH 2-3 SECONDS BLOTTING TIME

Electron Microscopy
Imaging
Microscope	model: FEI TECNAI F20
Details	THE DATA WERE COLLECTED WITH LEGINON AT SCRIPPS
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	120 kV
Electron dose	15 e/A**2
Illumination mode	LOW DOSE
Lens
Mode	BRIGHT FIELD
Magnification	calibrated: 148500 X
Cs	nominal: 2 mm
Nominal defocus	max: 3500 nm, min: 700 nm
Specimen holder
Temperature	95 Kelvin
Detector
Type	GATAN ULTRASCAN 4000 4K CCD CAMERA

Processing
2D projection selection
Number of particles	5500
Software name	SPIDER, IMAGIC
3D reconstruction
Actual pixel size	2.02 A/pix
CTF correction method	EACH PARTICLE WAS PHASE FLIPPED
Details	SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1998.(DEPOSITION ID: 10406).
Method	PROJECTION MATCHING
Nominal pixel size	2.02 A/pix
Resolution	8 A
3D fitting
Method	FLEXIBLE FITTING
Refinement Protocol	X-RAY
Refinement Space	REAL
Target criteria	CROSS-CORRELATION COEFFICIENT
3D fitting list
PDB entry ID	1OEL PDB-1oel
Refine
Ls d res high	8.00 A
ID	1
Refine hist
D res high	8.00
Total atoms	54075
Ligand atoms	231
Protein atoms	53844