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- PDB-9mmz: E. coli SR1 single-ring GroEL oligomer -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9mmz
TitleE. coli SR1 single-ring GroEL oligomer
ComponentsChaperonin GroEL
KeywordsCHAPERONE / Chaperone Inhibitor
Function / homology
Function and homology information


chaperonin ATPase / isomerase activity / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / ATP binding / metal ion binding / 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
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJohnson, S.M. / Chen, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120350 United States
CitationJournal: To Be Published
Title: Deciphering the unique mechanism whereby bis-sulfonamido-2-phenylbenzoxazole (PBZ) GroEL/ES inhibitors modulate chaperonin ATPase and client protein folding functions.
Authors: Stevens, M. / Doud, E. / Norambuena, J. / Tepper, K. / Trindl, C.A. / Carpenter, R. / Chapman, E. / Boyd, J.M. / Wells, C. / Chen, Q. / Johnson, S.M.
History
DepositionDec 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperonin GroEL
B: Chaperonin GroEL
C: Chaperonin GroEL
D: Chaperonin GroEL
E: Chaperonin GroEL
F: Chaperonin GroEL
H: Chaperonin GroEL


Theoretical massNumber of molelcules
Total (without water)400,8317
Polymers400,8317
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Chaperonin GroEL / 60 kDa chaperonin / Chaperonin-60 / Cpn60


Mass: 57261.539 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: groL, groEL, groL_1, A2J79_003959, A2J79_005474, A5U30_003693, ABE91_001090, ACN81_06325, ACU57_19295, B6R15_002033, B6R31_000859, BANRA_00147, BANRA_02830, BB545_11040, BCB93_001198, BG944_ ...Gene: groL, groEL, groL_1, A2J79_003959, A2J79_005474, A5U30_003693, ABE91_001090, ACN81_06325, ACU57_19295, B6R15_002033, B6R31_000859, BANRA_00147, BANRA_02830, BB545_11040, BCB93_001198, BG944_005198, BGM66_001100, BGZ_01627, BGZ_05100, BK300_24275, BK383_12940, BKL28_003536, BKL28_005489, BMT50_06320, BMT91_05495, BRV02_002050, BTB68_004143, BTQ06_07135, BvCmsKKP061_03324, BvCmsNSP007_04896, BvCmsSIP010_01340, BXT93_23590, C0P57_003473, C1Q91_002277, C2M16_07145, C2R31_001785, C2R31_005321, C3F40_14340, C6669_06700, C719_002796, C7B02_22870, C9160_20130, C9194_23880, C9Z68_08425, CCS08_01935, CF22_001662, CF22_005318, CG704_01665, CIG67_06440, CQ842_09470, CQ842_11950, CV83915_01888, CWS33_03390, D3C88_27260, D3G36_16020, D3G36_27385, D4N09_04290, D9D43_14725, D9E49_11975, D9J61_09370, DD762_21030, DL968_22275, DNQ45_22695, DNX30_08345, DNX30_30410, DS732_02495, DTL43_02185, DU321_10255, E2865_05408, E4K51_08915, E5H86_25825, E6D34_03900, EAI46_05875, ECs5124, EIA08_20145, EN85_000862, EPS76_03470, EPS97_10040, EWK56_08835, ExPECSC038_04651, F7F11_04220, F7N46_18305, F7N46_27130, F9413_14230, F9461_18160, F9461_28440, F9B07_06155, FGAF848_41910, FIJ20_10460, FJQ40_01790, FKO60_18130, FOI11_014910, FOI11_20770, FPI65_25535, FPS11_04035, FPS11_29800, FVB16_06060, FZU14_15570, G3V95_22465, G3W53_08890, G4A38_02930, G4A47_11060, GAI89_04545, GAJ12_10905, GKF66_07975, GNW61_00495, GNZ05_11940, GOP25_14290, GP711_17780, GP944_08950, GP954_08230, GP975_02890, GQE86_14145, GQM04_14160, GQM13_10590, GQM21_05675, GQN24_09575, GQN34_02395, GRC73_06265, GRW05_17640, GRW24_06445, GTP92_21420, GUC01_08885, HEP30_014195, HHH44_003373, HI055_001395, HI055_004873, HIE29_005290, HJQ60_002547, HJQ60_005759, HKA49_000870, HLX92_12540, HLZ39_23060, HLZ50_12865, HMV95_06875, HV109_21650, HV209_20120, HVV39_15060, HVW04_12630, HVW43_14140, HVY77_23275, I6H00_16320, I6H02_16535, IFC14_000451, IFC14_005433, IH772_04800, J5U05_001408, J8F57_000144, JNA68_20335, JNP96_02875, NCTC10082_01857, NCTC10089_04560, NCTC10418_06721, NCTC10764_04513, NCTC10767_00467, NCTC10865_05650, NCTC10974_05136, NCTC11112_02719, NCTC11181_01789, NCTC11341_03019, NCTC7927_05027, NCTC8333_05251, NCTC8500_05095, NCTC8621_04680, NCTC8622_02021, NCTC8959_04316, NCTC8960_02051, NCTC9044_02622, NCTC9045_05354, NCTC9073_03984, NCTC9077_05690, NCTC9081_01494, NCTC9117_05641, NCTC9702_05313, NCTC9706_01822, NOI85_20245, NY836_27345, OFN31_10965, OGM49_01575, P6223_004291, PWL68_003757, PWL68_005303, Q2V20_10495, Q2V64_07780, QDW62_23655, QO046_18850, R8G00_19495, R8O40_003300, R8O40_005491, RZR61_04445, SAMEA3472044_01554, SAMEA3472056_01662, V9Z47_22995, WR15_07175
Production host: Escherichia coli (E. coli) / References: UniProt: Q548M1, chaperonin ATPase
Has protein modificationN

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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: E. coli SR1 / Type: COMPLEX / Details: Single-ring oligomer of E. coli GroEL. / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 295199 / Symmetry type: POINT

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