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- EMDB-26122: Skd3, hexamer, filtered -

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Basic information

Entry
Database: EMDB / ID: EMD-26122
TitleSkd3, hexamer, filtered
Map dataGaussian filtered map
Sample
  • Complex: Skd3 bound to FITC-casein
    • Protein or peptide: Caseinolytic peptidase B protein homolog
    • Protein or peptide: Beta-casein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsAAA+ / cryoEM / CHAPERONE
Function / homology
Function and homology information


RIG-I signaling pathway / granulocyte differentiation / ATP-dependent protein disaggregase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / antiviral innate immune response / mitochondrial intermembrane space / cellular response to heat / ATP hydrolysis activity / mitochondrion / extracellular region ...RIG-I signaling pathway / granulocyte differentiation / ATP-dependent protein disaggregase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / antiviral innate immune response / mitochondrial intermembrane space / cellular response to heat / ATP hydrolysis activity / mitochondrion / extracellular region / ATP binding / cytoplasm
Similarity search - Function
Casein, beta / Casein, alpha/beta / Casein / Casein alpha/beta, conserved site / Caseins alpha/beta signature. / : / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein ...Casein, beta / Casein, alpha/beta / Casein / Casein alpha/beta, conserved site / Caseins alpha/beta signature. / : / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / ATPase, AAA-type, core / Ankyrin repeat-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Mitochondrial disaggregase / Beta-casein
Similarity search - Component
Biological speciesHomo sapiens (human) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsRizo AN / Cupo RR
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138690 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM099836 United States
CitationJournal: Cell Rep / Year: 2022
Title: Unique structural features govern the activity of a human mitochondrial AAA+ disaggregase, Skd3.
Authors: Ryan R Cupo / Alexandrea N Rizo / Gabriel A Braun / Eric Tse / Edward Chuang / Kushol Gupta / Daniel R Southworth / James Shorter /
Abstract: The AAA+ protein, Skd3 (human CLPB), solubilizes proteins in the mitochondrial intermembrane space, which is critical for human health. Skd3 variants with defective protein-disaggregase activity ...The AAA+ protein, Skd3 (human CLPB), solubilizes proteins in the mitochondrial intermembrane space, which is critical for human health. Skd3 variants with defective protein-disaggregase activity cause severe congenital neutropenia (SCN) and 3-methylglutaconic aciduria type 7 (MGCA7). How Skd3 disaggregates proteins remains poorly understood. Here, we report a high-resolution structure of a Skd3-substrate complex. Skd3 adopts a spiral hexameric arrangement that engages substrate via pore-loop interactions in the nucleotide-binding domain (NBD). Substrate-bound Skd3 hexamers stack head-to-head via unique, adaptable ankyrin-repeat domain (ANK)-mediated interactions to form dodecamers. Deleting the ANK linker region reduces dodecamerization and disaggregase activity. We elucidate apomorphic features of the Skd3 NBD and C-terminal domain that regulate disaggregase activity. We also define how Skd3 subunits collaborate to disaggregate proteins. Importantly, SCN-linked subunits sharply inhibit disaggregase activity, whereas MGCA7-linked subunits do not. These advances illuminate Skd3 structure and mechanism, explain SCN and MGCA7 inheritance patterns, and suggest therapeutic strategies.
History
DepositionFeb 1, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26122.png

Downloads & links

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Map

FileDownload / File: emd_26122.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGaussian filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 352 pix.
= 293.92 Å		0.84 Å/pix.
x 352 pix.
= 293.92 Å		0.84 Å/pix.
x 352 pix.
= 293.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum-0.037418228 - 0.4517004
Average (Standard dev.)0.006016917 (±0.034925647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 293.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Skd3 bound to FITC-casein

EntireName: Skd3 bound to FITC-casein
Components
  • Complex: Skd3 bound to FITC-casein
    • Protein or peptide: Caseinolytic peptidase B protein homolog
    • Protein or peptide: Beta-casein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: Skd3 bound to FITC-casein

SupramoleculeName: Skd3 bound to FITC-casein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Macromolecule #1: Caseinolytic peptidase B protein homolog

MacromoleculeName: Caseinolytic peptidase B protein homolog / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.115047 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GGSYSKSPSN KDAALLEAAR ANNMQEVSRL LSEGADVNAK HRLGWTALMV AAINRNNSVV QVLLAAGADP NLGDDFSSVY KTAKEQGIH SLEDGGQDGA SRHITNQWTS ALEFRRWLGL PAGVLITRED DFNNRLNNRA SFKGCTALHY AVLADDYRTV K ELLDGGAN ...String:
GGSYSKSPSN KDAALLEAAR ANNMQEVSRL LSEGADVNAK HRLGWTALMV AAINRNNSVV QVLLAAGADP NLGDDFSSVY KTAKEQGIH SLEDGGQDGA SRHITNQWTS ALEFRRWLGL PAGVLITRED DFNNRLNNRA SFKGCTALHY AVLADDYRTV K ELLDGGAN PLQRNEMGHT PLDYAREGEV MKLLRTSEAK YQEKQRKREA EERRRFPLEQ RLKEHIIGQE SAIATVGAAI RR KENGWYD EEHPLVFLFL GSSGIGKTEL AKQTAKYMHK DAKKGFIRLD MSEFQERHEV AKFIGSPPGY VGHEEGGQLT KKL KQCPNA VVLFDEVDKA HPDVLTIMLQ LFDEGRLTDG KGKTIDCKDA IFIMTSNVAS DEIAQHALQL RQEALEMSRN RIAE NLGDV QISDKITISK NFKENVIRPI LKAHFRRDEF LGRINEIVYF LPFCHSELIQ LVNKELNFWA KRAKQRHNIT LLWDR EVAD VLVDGYNVHY GARSIKHEVE RRVVNQLAAA YEQDLLPGGC TLRITVEDSD KQLLKSPELP SPQAEKRLPK LRLEII DKD SKTRRLDIRA PLHPEKVCNT I

UniProtKB: Mitochondrial disaggregase

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Macromolecule #2: Beta-casein

MacromoleculeName: Beta-casein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 24.759648 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)ARELEE LNVP GEIVE SLSSSEESIT RINKKIEKFQ SEEQQQTEDE LQDKIHPFAQ TQSLVYPFPG PIPNSLPQNI PPLTQTPVVV PPFLQ PEVM GVSKVKGAMA ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)ARELEE LNVP GEIVE SLSSSEESIT RINKKIEKFQ SEEQQQTEDE LQDKIHPFAQ TQSLVYPFPG PIPNSLPQNI PPLTQTPVVV PPFLQ PEVM GVSKVKGAMA PKHKEMPFPK YPVEPLTESQ SLTLTDVENL HLPLPLLQSW MHQPHQPLPP TVMFPPQSVL SLSQSK VLP VPQKAVPYPQ RDMPIQAFLL YQEPVLGPVR GPFPIIV

UniProtKB: Beta-casein

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / 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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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 4 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / 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: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 358000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7tts:
Skd3, hexamer, filtered

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