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- EMDB-26555: ClpAP complex bound to ClpS N-terminal extension, class IIb -

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Basic information

Entry
Database: EMDB / ID: EMD-26555
TitleClpAP complex bound to ClpS N-terminal extension, class IIb
Map data
Sample
  • Complex: AAA+ protease complex ClpAP bound to adaptor protein ClpS and GFP
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpA
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease adapter protein ClpS
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA+ protease / Adaptor / protein complex / CHAPERONE
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / protein catabolic process / peptidase activity / cellular response to heat / ATPase binding / serine-type endopeptidase activity ...endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / protein catabolic process / peptidase activity / cellular response to heat / ATPase binding / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / cytoplasm
Similarity search - Function
ATP-dependent Clp protease adaptor protein ClpS / ATP-dependent Clp protease ATP-binding subunit ClpA / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. ...ATP-dependent Clp protease adaptor protein ClpS / ATP-dependent Clp protease ATP-binding subunit ClpA / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ClpP/crotonase-like domain superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease adapter protein ClpS / ATP-dependent Clp protease ATP-binding subunit ClpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsKim S / Fei X / Sauer RT / Baker TA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Howard Hughes Medical Institute (HHMI) United States
Citation
Journal: Nat Struct Mol Biol / Year: 2022
Title: AAA+ protease-adaptor structures reveal altered conformations and ring specialization.
Authors: Sora Kim / Xue Fei / Robert T Sauer / Tania A Baker /
Abstract: ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here we present high-resolution cryo-EM structures of Escherichia coli ClpAPS complexes, showing how ClpA pore ...ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here we present high-resolution cryo-EM structures of Escherichia coli ClpAPS complexes, showing how ClpA pore loops interact with the ClpS N-terminal extension (NTE), which is normally intrinsically disordered. In two classes, the NTE is bound by a spiral of pore-1 and pore-2 loops in a manner similar to substrate-polypeptide binding by many AAA+ unfoldases. Kinetic studies reveal that pore-2 loops of the ClpA D1 ring catalyze the protein remodeling required for substrate delivery by ClpS. In a third class, D2 pore-1 loops are rotated, tucked away from the channel and do not bind the NTE, demonstrating asymmetry in engagement by the D1 and D2 rings. These studies show additional structures and functions for key AAA+ elements. Pore-loop tucking may be used broadly by AAA+ unfoldases, for example, during enzyme pausing/unloading.
#1: Journal: To Be Published
Title: ClpAP AAA+ Protease Adaptor Structures Reveal Pore-Loop Specialization
Authors: Kim S / Fei X / Sauer RT / Baker TA
History
DepositionMar 29, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26555.png

Downloads & links

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Map

FileDownload / File: emd_26555.map.gz / Format: CCP4 / Size: 24.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.87 Å/pix.
x 174 pix.
= 151.38 Å		0.87 Å/pix.
x 170 pix.
= 147.9 Å		0.87 Å/pix.
x 220 pix.
= 191.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.82
Minimum - Maximum-8.650321999999999 - 18.488299999999999
Average (Standard dev.)-0.000000000008782 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin636757
Dimensions170220174
Spacing174170220
CellA: 151.38 Å / B: 147.9 Å / C: 191.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : AAA+ protease complex ClpAP bound to adaptor protein ClpS and GFP

EntireName: AAA+ protease complex ClpAP bound to adaptor protein ClpS and GFP
Components
  • Complex: AAA+ protease complex ClpAP bound to adaptor protein ClpS and GFP
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpA
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease adapter protein ClpS
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: AAA+ protease complex ClpAP bound to adaptor protein ClpS and GFP

SupramoleculeName: AAA+ protease complex ClpAP bound to adaptor protein ClpS and GFP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: ATP-dependent Clp protease ATP-binding subunit ClpA

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 84.291758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLNQELELSL NMAFARAREH RHEFMTVEHL LLALLSNPSA REALEACSVD LVALRQELEA FIEQTTPVLP ASEEERDTQP TLSFQRVLQ RAVFHVQSSG RNEVTGANVL VAIFSEQESQ AAYLLRKHEV SRLDVVNFIS HGTRKDEPTQ SSDPGSQPNS E EQAGGEER ...String:
MLNQELELSL NMAFARAREH RHEFMTVEHL LLALLSNPSA REALEACSVD LVALRQELEA FIEQTTPVLP ASEEERDTQP TLSFQRVLQ RAVFHVQSSG RNEVTGANVL VAIFSEQESQ AAYLLRKHEV SRLDVVNFIS HGTRKDEPTQ SSDPGSQPNS E EQAGGEER TENFTTNLNQ LARVGGIDPL IGREKELERA IQVLCRRRKN NPLLVGESGV GKTAIAEGLA WRIVQGDVPE VM ADCTIYS LDIGSLLAGT KYRGDFEKRF KALLKQLEQD TNSILFIDEI HTIIGAGAAS GGQVDAANLI KPLLSSGKIR VIG STTYQE FSNIFEKDRA LARRFQKIDI TEPSIEETVQ IINGLKPKYE AHHDVRYTAK AVRAAVELAV KYINDRHLPD KAID VIDEA GARARLMPVS KRKKTVNVAD IESVVARIAR IPEKSVSQSD RDTLKNLGDR LKMLVFGQDK AIEALTEAIK MARAG LGHE HKPVGSFLFA GPTGVGKTEV TVQLSKALGI ELLRFDMSEY MERHTVSRLI GAPPGYVGFD QGGLLTDAVI KHPHAV LLL DEIEKAHPDV FNILLQVMDN GTLTDNNGRK ADFRNVVLVM TTNAGVRETE RKSIGLIHQD NSTDAMEEIK KIFTPEF RN RLDNIIWFDH LSTDVIHQVV DKFIVELQVQ LDQKGVSLEV SQEARNWLAE KGYDRAMGAR PMARVIQDNL KKPLANEL L FGSLVDGGQV TVALDKEKNE LTYGFQSAQK HKAEAAH

UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpA

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Macromolecule #2: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.660018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ALVPMVIEQT SRGERSFDIY SRLLKERVIF LTGQVEDHMA NLIVAQMLFL EAENPEKDIY LYINSPGGVI TAGMSIYDTM QFIKPDVST ICMGQAASMG AFLLTAGAKG KRFCLPNSRV MIHQPLGGYQ GQATDIEIHA REILKVKGRM NELMALHTGQ S LEQIERDT ...String:
ALVPMVIEQT SRGERSFDIY SRLLKERVIF LTGQVEDHMA NLIVAQMLFL EAENPEKDIY LYINSPGGVI TAGMSIYDTM QFIKPDVST ICMGQAASMG AFLLTAGAKG KRFCLPNSRV MIHQPLGGYQ GQATDIEIHA REILKVKGRM NELMALHTGQ S LEQIERDT ERDRFLSAPE AVEYGLVDSI LTHRNRSHHH HHH

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #3: ATP-dependent Clp protease adapter protein ClpS

MacromoleculeName: ATP-dependent Clp protease adapter protein ClpS / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.193038 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGKTNDWLDF DQLAEEKVRD ALKPPSMYKV ILVNDDYTPM EFVIDVLQKF FSYDVERATQ LMLAVHYQGK AICGVFTAEV AETKVAMVN KYARENEHPL LCTLEKA

UniProtKB: ATP-dependent Clp protease adapter protein ClpS

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 9 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.5 µm / Nominal defocus min: -0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

20406

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 43431
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 6 / Software - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7uiw:
ClpAP complex bound to ClpS N-terminal extension, class IIb

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