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- PDB-2c7e: REVISED ATOMIC STRUCTURE FITTING INTO A GROEL(D398A)-ATP7 CRYO-EM... -

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Basic information

Entry
Database: PDB / ID: 2c7e
TitleREVISED ATOMIC STRUCTURE FITTING INTO A GROEL(D398A)-ATP7 CRYO-EM MAP (EMD 1047)
Components60 KDA CHAPERONIN
KeywordsCELL 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 / : / 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 / : / 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 / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Chaperonin GroEL / Chaperonin GroEL
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14.9 Å
AuthorsRanson, N.A. / Farr, G.W. / Roseman, A.M. / Gowen, B. / Fenton, W.A. / Horwich, A.L. / Saibil, H.R.
CitationJournal: 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
DepositionNov 22, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 16, 2006ID: 1GR6
Revision 1.0Feb 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.5Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.6May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine.ls_d_res_high / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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.

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-1047
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Structure viewerMolecule:
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Assembly

Deposited unit
A: 60 KDA CHAPERONIN
B: 60 KDA CHAPERONIN
C: 60 KDA CHAPERONIN
D: 60 KDA CHAPERONIN
E: 60 KDA CHAPERONIN
F: 60 KDA CHAPERONIN
G: 60 KDA CHAPERONIN
H: 60 KDA CHAPERONIN
I: 60 KDA CHAPERONIN
J: 60 KDA CHAPERONIN
K: 60 KDA CHAPERONIN
L: 60 KDA CHAPERONIN
M: 60 KDA CHAPERONIN
N: 60 KDA CHAPERONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)804,63235
Polymers800,63814
Non-polymers3,99421
Water75742
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
60 KDA CHAPERONIN / GROEL / PROTEIN CPN60 / GROEL 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 / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGROEL IS A HOMOOLIGOMER OF FOURTEEN SUBUNITS ARRANGED IN A DOUBLE RING STRUCTURE. ENGINEERED ...GROEL IS A HOMOOLIGOMER OF FOURTEEN SUBUNITS ARRANGED IN A DOUBLE RING STRUCTURE. ENGINEERED RESIDUE IN CHAIN A, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN A, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN B, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN B, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN C, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN C, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN D, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN D, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN E, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN E, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN F, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN F, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN G, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN G, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN H, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN H, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN I, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN I, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN J, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN J, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN K, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN K, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN L, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN L, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN M, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN M, ALA 125 TO VAL ENGINEERED RESIDUE IN CHAIN N, ARG 12 TO GLY ENGINEERED RESIDUE IN CHAIN N, ALA 125 TO VAL MUTATIONS ARE IN FITTED COORDINATES NOT THE MOLECULE WHICH GENERATED THE EM MAP WHICH WAS GROEL(D398A)
Sequence detailsMET 1 IN ALL CHAINS HAS BEEN POST-TRANSLATIONALLY REMOVED.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GROEL(D398A)-ATP / Type: COMPLEX
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 X / Calibrated magnification: 37604 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 160
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1DockEMmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: FULL CORRECTION ON 2D CLASS AVERAGES
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionMethod: 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 buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--LOCAL CORRELATION USING DOCKEM
RefinementHighest resolution: 14.9 Å
Refinement stepCycle: LAST / Highest resolution: 9.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53970 0 231 42 54243

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