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- PDB-3zpz: Visualizing GroEL-ES in the Act of Encapsulating a Non-Native Sub... -

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Basic information

Entry
Database: PDB / ID: 3zpz
TitleVisualizing GroEL-ES in the Act of Encapsulating a Non-Native Substrate Protein
Components
  • 10 KDA CHAPERONIN
  • 60 KDA CHAPERONIN
KeywordsCHAPERONE / PROTEIN FOLDING / HETEROGENEITY
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / 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 / GroES-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chaperonin GroEL / Co-chaperonin GroES
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
ESCHERICHIA COLI K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsChen, D.-H. / Madan, D. / Weaver, J. / Lin, Z. / Schroder, G.F. / Chiu, W. / Rye, H.S.
CitationJournal: Cell / Year: 2013
Title: Visualizing GroEL/ES in the act of encapsulating a folding protein.
Authors: Dong-Hua Chen / Damian Madan / Jeremy Weaver / Zong Lin / Gunnar F Schröder / Wah Chiu / Hays S Rye /
Abstract: The GroEL/ES chaperonin system is required for the assisted folding of many proteins. How these substrate proteins are encapsulated within the GroEL-GroES cavity is poorly understood. Using symmetry- ...The GroEL/ES chaperonin system is required for the assisted folding of many proteins. How these substrate proteins are encapsulated within the GroEL-GroES cavity is poorly understood. Using symmetry-free, single-particle cryo-electron microscopy, we have characterized a chemically modified mutant of GroEL (EL43Py) that is trapped at a normally transient stage of substrate protein encapsulation. We show that the symmetric pattern of the GroEL subunits is broken as the GroEL cis-ring apical domains reorient to accommodate the simultaneous binding of GroES and an incompletely folded substrate protein (RuBisCO). The collapsed RuBisCO folding intermediate binds to the lower segment of two apical domains, as well as to the normally unstructured GroEL C-terminal tails. A comparative structural analysis suggests that the allosteric transitions leading to substrate protein release and folding involve concerted shifts of GroES and the GroEL apical domains and C-terminal tails.
History
DepositionMar 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id
Revision 1.2May 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 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-2325
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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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
O: 10 KDA CHAPERONIN
P: 10 KDA CHAPERONIN
Q: 10 KDA CHAPERONIN
R: 10 KDA CHAPERONIN
S: 10 KDA CHAPERONIN
T: 10 KDA CHAPERONIN
U: 10 KDA CHAPERONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)852,45535
Polymers849,29421
Non-polymers3,16114
Water00
1


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

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Components

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


Mass: 55463.387 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: A GROEL VARIANT IN WHICH THE ENDOGENOUS CYS RESIDUES (138,458,519) HAVE BEEN CHANGED TO ALA (GROELCYS0) WAS MODIFIED TO CONTAIN TWO ADDITIONAL MUTATIONS D398A AND S43C. THE D398A MUTATION ...Details: A GROEL VARIANT IN WHICH THE ENDOGENOUS CYS RESIDUES (138,458,519) HAVE BEEN CHANGED TO ALA (GROELCYS0) WAS MODIFIED TO CONTAIN TWO ADDITIONAL MUTATIONS D398A AND S43C. THE D398A MUTATION PREVENTS ATP HYDROLYSIS BY GROEL, WHILE THE S43C MUTATION, LOCATED AT THE TIP OF STEM LOOP AT THE BOTTOM OF THE GROEL CAVITY, PERMITS THE COVALENT ATTACHMENT OF N-1-PYRENE MALEIMIDE TO THIS POSITION.
Source: (gene. exp.) ESCHERICHIA COLI BL21 (bacteria) / Plasmid: PACYC / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6F5
#2: Protein
10 KDA CHAPERONIN / GROES PROTEIN / PROTEIN CPN10


Mass: 10400.938 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PACYC / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6F9
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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 VARIANT EL43PY CAPPED BY GROES WITH THE ASSISTANCE OF NUCLEOTIDE ATP
Type: COMPLEX
Buffer solutionName: 50 MM HEPES, 5 MM KOAC, 10 MM MG(OAC)2, 2 MM DTT / pH: 7.6 / Details: 50 MM HEPES, 5 MM KOAC, 10 MM MG(OAC)2, 2 MM DTT
SpecimenConc.: 6.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, TEMPERATURE- 98, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 1 SECOND BEFORE PLUNGING,

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Electron microscopy imaging

MicroscopyModel: JEOL KYOTO-3000SFF / Date: Mar 7, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal magnification: 60000 X / Calibrated magnification: 61060 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1200 nm / Cs: 1.6 mm
Specimen holderTemperature: 11 K
Image recordingElectron dose: 36 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 390

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Processing

EM software
IDNameVersionCategory
1DireXmodel fitting
2EMAN13D reconstruction
CTF correctionDetails: EACH MICROGRAPH
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionMethod: FOURIER METHODS / Resolution: 8.9 Å / Num. of particles: 8372 / Nominal pixel size: 2.12 Å / Actual pixel size: 2.08 Å
Magnification calibration: THE RMSD BETWEEN ALL EQUATORIAL DOMAINS OF THE FITTED MODELS AND THE X-RAY STRUCTURE OF THE GROEL-GROES-ADP COMPLEX WAS CALCULATED AND THE OPTIMAL PIXEL SIZE WAS CHOSEN AS ...Magnification calibration: THE RMSD BETWEEN ALL EQUATORIAL DOMAINS OF THE FITTED MODELS AND THE X-RAY STRUCTURE OF THE GROEL-GROES-ADP COMPLEX WAS CALCULATED AND THE OPTIMAL PIXEL SIZE WAS CHOSEN AS THE ONE THAT LEADS TO THE SMALLEST RMSD VALUE
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2325. (DEPOSITION ID: 11454).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 1AON

1aon


Accession code: 1AON / Source name: PDB / Type: experimental model
RefinementHighest resolution: 8.9 Å
Refinement stepCycle: LAST / Highest resolution: 8.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59080 0 196 0 59276

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