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- PDB-5are: Bovine mitochondrial ATP synthase state 1b -

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Entry
Database: PDB / ID: 5are
TitleBovine mitochondrial ATP synthase state 1b
Components
  • (ATP SYNTHASE F(0) COMPLEX SUBUNIT ...) x 2
  • (ATP SYNTHASE SUBUNIT ...) x 8
  • ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
KeywordsHYDROLASE / ATP SYNTHASE / ROTARY ATPASE
Function / homology
Function and homology information


Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / : / : / proton-transporting ATP synthase complex / : / : ...Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / : / : / proton-transporting ATP synthase complex / : / : / : / Mitochondrial protein degradation / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / aerobic respiration / proton transmembrane transport / ADP binding / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial ...ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase F(0) complex subunit C1, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsZhou, A. / Rohou, A. / Schep, D.G. / Bason, J.V. / Montgomery, M.G. / Walker, J.E. / Grigorieff, N. / Rubinstein, J.L.
CitationJournal: Elife / Year: 2015
Title: Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM.
Authors: Anna Zhou / Alexis Rohou / Daniel G Schep / John V Bason / Martin G Montgomery / John E Walker / Nikolaus Grigorieff / John L Rubinstein /
Abstract: Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic ...Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases.
History
DepositionSep 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Apr 19, 2017Group: Other
Revision 1.3Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4May 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 / refine / struct_sheet
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 / _refine.ls_d_res_high / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN **-STRANDED BARREL THIS IS REPRESENTED BY A **-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 0-STRANDED BARREL THIS IS REPRESENTED BY A 1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 0-STRANDED BARREL THIS IS REPRESENTED BY A 1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. 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: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
B: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
C: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
D: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
E: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
F: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
G: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
H: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
I: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
J: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
K: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
L: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
M: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
N: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
O: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
P: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
Q: ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL
T: ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIAL
U: ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL
V: ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
W: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)518,89322
Polymers518,89322
Non-polymers00
Water00
1


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

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Components

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ATP SYNTHASE SUBUNIT ... , 8 types, 12 molecules ABCDEFGHISUW

#1: Protein ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL


Mass: 55301.207 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 44-553 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIA / Tissue: HEART / References: UniProt: P19483
#2: Protein ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL


Mass: 51757.836 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 47-528 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIA / Tissue: HEART
References: UniProt: P00829, H+-transporting two-sector ATPase
#3: Protein ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL / F-ATPASE GAMMA SUBUNIT


Mass: 30300.760 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-298 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIA / Tissue: HEART / References: UniProt: P05631
#4: Protein ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL / F-ATPASE DELTA SUBUNIT


Mass: 15074.813 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 23-168 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIA / Tissue: HEART / References: UniProt: P05630
#5: Protein/peptide ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL / ATPASE SUBUNIT EPSILON


Mass: 5662.693 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-51 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIA / Tissue: HEART / References: UniProt: P05632
#7: Protein ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL / OLIGOMYCIN SENSITIVITY CONFERRAL PROTEIN / OSCP


Mass: 20989.803 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: HEART / Organ: MITOCHONDRIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13621
#9: Protein ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL / ATPASE SUBUNIT D


Mass: 14167.169 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: HEART / Organ: MITOCHONDRIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P13620
#11: Protein ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL


Mass: 23717.578 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 10-226 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIA / Tissue: HEART / References: UniProt: P00847

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ATP SYNTHASE F(0) COMPLEX SUBUNIT ... , 2 types, 9 molecules JKLMNOPQT

#6: Protein
ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL / ATP SYNTHASE LIPID-BINDING PROTEIN / ATP SYNTHASE PROTEOLIPID P1 / ATPASE PROTEIN 9 / ATPASE SUBUNIT C


Mass: 7293.593 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 63-134 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIA / Tissue: HEART / References: UniProt: P32876
#8: Protein ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIAL / ATP SYNTHASE SUBUNIT B / ATPASE SUBUNIT B


Mass: 20335.625 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 76-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: HEART / Organ: MITOCHONDRIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P13619

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Protein , 1 types, 1 molecules V

#10: Protein ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL / ATPASE SUBUNIT F6


Mass: 9118.253 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 32-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: HEART / Organ: MITOCHONDRIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P02721

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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: BOVINE MITOCHONDRIAL ATP SYNTHASE / Type: COMPLEX
Buffer solutionName: 20 MM TRIS-HCL, 100 MM NACL, 10% (V/V) DODECYLMALTOSIDE, 2 MM ATP, 0.02% (WT/V) NAN3
pH: 7.2
Details: 20 MM TRIS-HCL, 100 MM NACL, 10% (V/V) DODECYLMALTOSIDE, 2 MM ATP, 0.02% (WT/V) NAN3
SpecimenConc.: 8 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-PROPANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 27 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Mar 15, 2015
Details: K2 SUMMIT DIRECT DETECTOR DEVICE (GATAN INC.) OPERATED IN SUPER- RESOLUTION MODE WITH A 1.64 ANGSTROM PHYSICAL PIXEL AND 0. 82 ANGSTROM SUPER- RESOLUTION PIXEL. WITH NO SPECIMEN PRESENT, THE ...Details: K2 SUMMIT DIRECT DETECTOR DEVICE (GATAN INC.) OPERATED IN SUPER- RESOLUTION MODE WITH A 1.64 ANGSTROM PHYSICAL PIXEL AND 0. 82 ANGSTROM SUPER- RESOLUTION PIXEL. WITH NO SPECIMEN PRESENT, THE RATE OF EXPOSURE OF THE DETECTOR WAS 8 ELECTRONS PER PIXEL PER SECOND. EXPOSURE- FRACTIONATED MOVIES OF 20.1 S WERE RECORDED AS STACKS OF 67 FRAMES, SO THAT SELECTED SPECIMEN AREAS WERE EXPOSED WITH A TOTAL OF 60.3 ELECTRONS PER SQUARE ANGSTROM.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 18000 X / Calibrated magnification: 30487 X / Nominal defocus max: 4100 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderTemperature: 80 K
Image recordingElectron dose: 60.3 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)

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Processing

EM software
IDNameCategory
1MDFFmodel fitting
2UCSF Chimeramodel fitting
3FREALIGN3D reconstruction
4RELION3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING AND MAXIMUM LIKELIHOOD CLASSIFICATION
Resolution: 6.7 Å / Num. of particles: 22935
Details: THE A SUBUNIT WAS MODELED USING EVOLUTIONARY COVARIANCE. THE N-TERMINAL TRANSMEMBRANE HELICES OF THE B SUBUNIT WERE MODELED BASED ON TRANSMEMBRANE HELIX PREDICTIONS. SUBMISSION BASED ON ...Details: THE A SUBUNIT WAS MODELED USING EVOLUTIONARY COVARIANCE. THE N-TERMINAL TRANSMEMBRANE HELICES OF THE B SUBUNIT WERE MODELED BASED ON TRANSMEMBRANE HELIX PREDICTIONS. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3165. (DEPOSITION ID: 13793).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Details: METHOD--FLEXIBLE FITTING
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12WSS

2wss

12WSS1PDBexperimental model
22XND

2xnd

12XND2PDBexperimental model
32CLY

2cly

12CLY3PDBexperimental model
RefinementHighest resolution: 6.7 Å
Refinement stepCycle: LAST / Highest resolution: 7.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18545 0 0 0 18545

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