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Yorodumi- PDB-2c7e: REVISED ATOMIC STRUCTURE FITTING INTO A GROEL(D398A)-ATP7 CRYO-EM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c7e | |||||||||
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Title | REVISED ATOMIC STRUCTURE FITTING INTO A GROEL(D398A)-ATP7 CRYO-EM MAP (EMD 1047) | |||||||||
Components | 60 KDA CHAPERONIN | |||||||||
Keywords | CELL CYCLE / ATP-BINDING / CHAPERONE / CHAPERONIN / D398A / HP60 CLASS / CELL DIVISION / NUCLEOTIDE-BINDING / PHOSPHORYLATION | |||||||||
Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14.9 Å | |||||||||
Authors | Ranson, N.A. / Farr, G.W. / Roseman, A.M. / Gowen, B. / Fenton, W.A. / Horwich, A.L. / Saibil, H.R. | |||||||||
Citation | Journal: Cell / Year: 2001 Title: ATP-bound states of GroEL captured by cryo-electron microscopy. Authors: N A Ranson / G W Farr / A M Roseman / B Gowen / W A Fenton / A L Horwich / H R Saibil / Abstract: The chaperonin GroEL drives its protein-folding cycle by cooperatively binding ATP to one of its two rings, priming that ring to become folding-active upon GroES binding, while simultaneously ...The chaperonin GroEL drives its protein-folding cycle by cooperatively binding ATP to one of its two rings, priming that ring to become folding-active upon GroES binding, while simultaneously discharging the previous folding chamber from the opposite ring. The GroEL-ATP structure, determined by cryo-EM and atomic structure fitting, shows that the intermediate domains rotate downward, switching their intersubunit salt bridge contacts from substrate binding to ATP binding domains. These observations, together with the effects of ATP binding to a GroEL-GroES-ADP complex, suggest structural models for the ATP-induced reduction in affinity for polypeptide and for cooperativity. The model for cooperativity, based on switching of intersubunit salt bridge interactions around the GroEL ring, may provide general insight into cooperativity in other ring complexes and molecular machines. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2c7e.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2c7e.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 2c7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/2c7e ftp://data.pdbj.org/pub/pdb/validation_reports/c7/2c7e | HTTPS FTP |
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-Related structure data
Related structure data | 1047MC 1042C 1046C 1gr5C 1gruC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 57188.410 Da / Num. of mol.: 14 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P06139, UniProt: P0A6F5*PLUS #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ATP / #5: Water | ChemComp-HOH / | Compound details | GROEL IS A HOMOOLIGOMER OF FOURTEEN SUBUNITS ARRANGED IN A DOUBLE RING STRUCTURE. ENGINEERED ...GROEL IS A HOMOOLIGOM | Sequence details | MET 1 IN ALL CHAINS HAS BEEN POST-TRANSLATIO | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: GROEL(D398A)-ATP / Type: COMPLEX |
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Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 X / Calibrated magnification: 37604 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm |
Specimen holder | Temperature: 100 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 160 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: FULL CORRECTION ON 2D CLASS AVERAGES | ||||||||||||
Symmetry | Point symmetry: D7 (2x7 fold dihedral) | ||||||||||||
3D reconstruction | Method: PROJECTION MATCHING-BASED ANGULAR REFINEMENT AND ITERATIVE ALGEBRAIC RECONSTRUCTION IN SPIDER Resolution: 14.9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 6404 / Actual pixel size: 1.86 Å Details: RIGID BODY FITTING IN URO, AFTER A 4 PER CENT MAGNIFICATION CORRECTION BEING APPLIED TO THE EM MAP. THIS SUBMISSION REPLACES PREVIOUS ENTRY 1GR6 Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--LOCAL CORRELATION USING DOCKEM | ||||||||||||
Refinement | Highest resolution: 9.7 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9.7 Å
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