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- PDB-8deh: Ankyrin domain of SKD3 -

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Basic information

Entry
Database: PDB / ID: 8deh
TitleAnkyrin domain of SKD3
ComponentsCaseinolytic peptidase B protein homolog
KeywordsHYDROLASE / mitochondria / CHAPERONE
Function / homology
Function and homology information


granulocyte differentiation / RIG-I signaling pathway / ATP-dependent protein disaggregase activity / antiviral innate immune response / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mitochondrial intermembrane space / cellular response to heat / ATP hydrolysis activity / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
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 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ATPase, AAA-type, core / ankyrin repeats ...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 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ATPase, AAA-type, core / ankyrin repeats / Ankyrin repeat / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.815 Å
AuthorsLee, S. / Tsai, F.T.F.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM142143 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK115454 United States
Robert A. Welch FoundationQ-1530-20190330 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR140038 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10-OD030246 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of impaired disaggregase function in the oxidation-sensitive SKD3 mutant causing 3-methylglutaconic aciduria.
Authors: Lee, S. / Lee, S.B. / Sung, N. / Xu, W.W. / Chang, C. / Kim, H.E. / Catic, A. / Tsai, F.T.F.
History
DepositionJun 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caseinolytic peptidase B protein homolog


Theoretical massNumber of molelcules
Total (without water)24,9471
Polymers24,9471
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.284, 61.130, 47.571
Angle α, β, γ (deg.)90.000, 106.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Caseinolytic peptidase B protein homolog / Suppressor of potassium transport defect 3


Mass: 24946.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SNKDAALLEAARANNMQEVSRLLSEGADVNAKHRLGWTALMVAAINRNNSVVQVLLAAGADPNLG DDFSSVYKTAKEQGIHSLEDGGQDGASRHITNQWTSALEFRRWLGLPAGVLITREDDFNNRLNNR ...Details: SNKDAALLEAARANNMQEVSRLLSEGADVNAKHRLGWTALMVAAINRNNSVVQVLLAAGADPNLG DDFSSVYKTAKEQGIHSLEDGGQDGASRHITNQWTSALEFRRWLGLPAGVLITREDDFNNRLNNR ASFKGCTALHYAVLADDYRTVKELLDGGANPLQRNEMGHTPLDYAREGEVMKLLRTSEAKYQEKQ RKREAEERRRFPLEQRLKEHIIGQE
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPB, HSP78, SKD3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H078, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM EPPS pH 8.0, 35% (v/v) PEP426, and 250 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.815→50 Å / Num. obs: 20905 / % possible obs: 99.1 % / Redundancy: 4.7 % / Rpim(I) all: 0.059 / Rsym value: 0.122 / Net I/σ(I): 9.9
Reflection shellResolution: 1.815→1.88 Å / Num. unique obs: 1015 / Rpim(I) all: 0.328 / Rsym value: 0.578

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SBC-Collect2data collection
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
WARPmodel building
PHENIX3.27refinement
RefinementMethod to determine structure: SAD / Resolution: 1.815→45.668 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1894 939 4.93 %
Rwork0.1633 18092 -
obs0.1645 19031 88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.81 Å2 / Biso mean: 25.9808 Å2 / Biso min: 5.97 Å2
Refinement stepCycle: final / Resolution: 1.815→45.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 0 155 1606
Biso mean---37.67 -
Num. residues----185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8152-1.91090.2891700.2136133746
1.9109-2.03070.21561120.1953233980
2.0307-2.18740.22571530.1799277595
2.1874-2.40760.1931580.166290199
2.4076-2.75590.1751670.1555286099
2.7559-3.4720.17781490.1555292199
3.472-45.6680.17751300.1551295998
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19620.1688-0.07970.26450.02780.16470.00090.0250.020.01110.0073-0.09880.0295-0.02170.01460.05630.0202-0.00690.07420.0020.0705-3.295937.48224.9039
20.0029-0.00070.0029-0.0025-0.00080.0073-0.2255-0.03810.02280.134-0.05980.19360.1507-0.0789-00.20830.01650.05410.1857-0.05520.2458-27.972142.698137.7018
30.013-0.00280.0097-0.0022-0.00670.00570.0951-0.0285-0.20570.1207-0.03270.25380.1591-0.1137-00.12410.01240.00370.1455-0.02010.2063-28.848134.809632.9029
40.52460.0121-0.0160.31530.07340.1433-0.0185-0.0856-0.38730.2151-0.16340.2049-0.00960.0063-0.08630.1210.03670.03230.0771-0.00040.0457-15.299728.974533.9936
50.1433-0.03950.01850.09060.0610.1825-0.28190.2741-0.3953-0.0178-0.61980.1269-0.062-0.0785-0.33660.2254-0.09260.0971-0.06480.3530.0338-10.873218.832341.4343
60.01280.01980.00580.01280.00710.0215-0.068-0.04470.24170.1555-0.1589-0.24060.0094-0.076-0.00310.0796-0.0439-0.05310.19630.03490.2419-3.695513.27864.8365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 129 through 201 )A129 - 201
2X-RAY DIFFRACTION2chain 'A' and (resid 202 through 232 )A202 - 232
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 260 )A233 - 260
4X-RAY DIFFRACTION4chain 'A' and (resid 261 through 309 )A261 - 309
5X-RAY DIFFRACTION5chain 'A' and (resid 310 through 329 )A310 - 329
6X-RAY DIFFRACTION6chain 'A' and (resid 330 through 345 )A330 - 345

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