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- PDB-2c7c: FITTED COORDINATES FOR GROEL-ATP7-GROES CRYO-EM COMPLEX (EMD-1180) -

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Basic information

Entry
Database: PDB / ID: 2c7c
TitleFITTED COORDINATES FOR GROEL-ATP7-GROES CRYO-EM COMPLEX (EMD-1180)
Descriptor60 KDA CHAPERONIN
10 KDA CHAPERONIN MOLECULE: GROES
PROTEIN CPN10
GROES PROTEIN
KeywordsCHAPERONE / ATP-BINDING / ATOMIC STRUCTURE FITTING / CELL CYCLE / CELL DIVISION / CHAPERONIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (7.7 Å resolution / Particle / Single particle)
AuthorsRanson, N.A. / Clare, D.K. / Farr, G.W. / Houldershaw, D. / Horwich, A.L. / Saibil, H.R.
CitationNat. Struct. Mol. Biol., 2006, 13, 147-152

Nat. Struct. Mol. Biol., 2006, 13, 147-152 StrPapers
Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes.
Neil A Ranson / Daniel K Clare / George W Farr / David Houldershaw / Arthur L Horwich / Helen R Saibil

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 22, 2005 / Release: Jan 25, 2006
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 25, 2006Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Aug 23, 2017Structure modelData collectionem_software_em_software.fitting_id / _em_software.image_processing_id
Remark 700 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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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 MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
P: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
Q: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
R: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
S: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
T: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
U: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN


Theoretical massNumber of molelcules
Total (without water)874,45421
Polyers874,45421
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)62390
ΔGint (kcal/M)-390.12
Surface area (Å2)321960
MethodPISA

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Components

#1: Polypeptide(L)
60 KDA CHAPERONIN / GROEL / PROTEIN CPN60 / GROEL PROTEIN


Mass: 57260.504 Da / Num. of mol.: 14
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P0A6F5

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)
10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN


Mass: 10400.938 Da / Num. of mol.: 7
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P0A6F9

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: GROEL-ATP7-GROES / Type: COMPLEX
Buffer solutionName: 12.5MM HEPES, 5MM KCL, 5MM MGCL2 / Details: 12.5MM HEPES, 5MM KCL, 5MM MGCL2 / pH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Nominal defocus max: 3200 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTemperature: 100 kelvins
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 189
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
1UROMODEL FITTING1
2IMAGICRECONSTRUCTION1
3SPIDERRECONSTRUCTION1
CTF correctionDetails: FULL CORRECTION ON 2D CLASS AVERAGES
SymmetryPoint symmetry: C7
3D reconstructionMethod: PROJECTION MATCHING-BASED ANGULAR REFINEMENT OF MSA GENERATED CLASSES. ITERATIVE ALGEBRAIC RECONSTRUCTION IN SPIDER.
Resolution: 7.7 Å / Number of particles: 16281 / Nominal pixel size: 1.4
Details: RECIPROCAL SPACE FITTING OF SEVEN INDEPENDENT RIGID BODIES WITH URO. FITTED ENTITIES WERE GROEL EQUATORIAL (RESIDUES 3-136 AND 410-524), INTERMEDIATE (RESIDUES 137-192 AND 374-409) AND APICAL (RESIDUES 192-373) DOMAINS, PLUS A GROES SUBUNIT. THE MAP INTO WHICH THESE COORDINATES WERE FITTED IS AVAILABLE AT THE EMD (EMD-1180)
Symmetry type: POINT
Atomic model buildingDetails: METHOD--RECIPROCAL SPACE FITTING IN URO / Ref protocol: OTHER
Least-squares processHighest resolution: 7.7 Å
Refine hist #LASTHighest resolution: 7.7 Å
Number of atoms included #LASTProtein: 57946 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 57946

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