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- PDB-5vsz: Structure of the Ubl domain of Sacsin mutant L78M -

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Basic information

Entry
Database: PDB / ID: 5vsz
TitleStructure of the Ubl domain of Sacsin mutant L78M
ComponentsSacsin
KeywordsCHAPERONE / ubiquitin-like
Function / homology
Function and homology information


negative regulation of inclusion body assembly / cell body fiber / proteasome binding / Hsp70 protein binding / protein folding / protein-folding chaperone binding / axon / dendrite / mitochondrion / identical protein binding ...negative regulation of inclusion body assembly / cell body fiber / proteasome binding / Hsp70 protein binding / protein folding / protein-folding chaperone binding / axon / dendrite / mitochondrion / identical protein binding / nucleus / cytoplasm
Similarity search - Function
HEPN domain profile. / Higher Eukarytoes and Prokaryotes Nucleotide-binding domain / HEPN domain / HEPN domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Histidine kinase/HSP90-like ATPase superfamily / Ubiquitin family / Ubiquitin domain profile. ...HEPN domain profile. / Higher Eukarytoes and Prokaryotes Nucleotide-binding domain / HEPN domain / HEPN domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Histidine kinase/HSP90-like ATPase superfamily / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsTrempe, J.-F. / Pande, H. / Shenker, S. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
ARSACS Foundation Canada
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structures of ubiquitin-like (Ubl) and Hsp90-like domains of sacsin provide insight into pathological mutations.
Authors: Menade, M. / Kozlov, G. / Trempe, J.F. / Pande, H. / Shenker, S. / Wickremasinghe, S. / Li, X. / Hojjat, H. / Dicaire, M.J. / Brais, B. / McPherson, P.S. / Wong, M.J.H. / Young, J.C. / Gehring, K.
History
DepositionMay 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sacsin
B: Sacsin


Theoretical massNumber of molelcules
Total (without water)19,8672
Polymers19,8672
Non-polymers00
Water34219
1
A: Sacsin


Theoretical massNumber of molelcules
Total (without water)9,9331
Polymers9,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sacsin


Theoretical massNumber of molelcules
Total (without water)9,9331
Polymers9,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.140, 61.450, 91.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sacsin / / DnaJ homolog subfamily C member 29 / DNAJC29


Mass: 9933.280 Da / Num. of mol.: 2 / Fragment: Ubl domain (UNP residues 2-85) / Mutation: L78M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SACS, KIAA0730 / Plasmid: pGEX-6p1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZJ4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 1.85 Å3/Da / Density % sol: 33.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.1 M bicine, 0.25 M NaCl, 1 mM lead acetate, 10% glycerol, pH 8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.97873, 0.97921
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 11, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978731
20.979211
30.964261
ReflectionResolution: 2.4→45.785 Å / Num. all: 5927 / Num. obs: 5927 / % possible obs: 98.9 % / Redundancy: 14 % / Biso Wilson estimate: 56.06 Å2 / Rpim(I) all: 0.02 / Rrim(I) all: 0.076 / Rsym value: 0.061 / Net I/av σ(I): 8.2 / Net I/σ(I): 24.8 / Num. measured all: 82884
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.4-2.5314.50.4981.50.1390.5340.49898.7
2.53-2.6814.30.3022.50.0850.3280.30299
2.68-2.8714.40.1943.90.0550.2120.19499.1
2.87-3.114.20.1146.50.0340.1280.11499.3
3.1-3.3914.20.0799.10.0240.0910.07999.1
3.39-3.814.10.05611.40.0170.0660.05699.3
3.8-4.3813.80.04713.60.0150.0570.04799.1
4.38-5.3713.50.043140.0140.0540.04399.8
5.37-7.59130.04514.10.0180.0650.04599.6
7.59-30.72510.50.0512.50.0220.0750.0591.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.16data scaling
SOLVEphasing
RESOLVEphasing
PDB_EXTRACT3.22data extraction
DENZOdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.129 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.18
RfactorNum. reflection% reflection
Rfree0.2842 270 4.56 %
Rwork0.2185 --
obs0.2215 5923 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.8 Å2 / Biso mean: 64.8079 Å2 / Biso min: 37.66 Å2
Refinement stepCycle: final / Resolution: 2.4→29.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 0 19 1079
Biso mean---57.48 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091090
X-RAY DIFFRACTIONf_angle_d1.0941485
X-RAY DIFFRACTIONf_chiral_restr0.042174
X-RAY DIFFRACTIONf_plane_restr0.005182
X-RAY DIFFRACTIONf_dihedral_angle_d13.15367
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4002-3.02350.34721470.2582761290899
3.0235-29.13110.26641230.20872892301598
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)
17.7881-4.1884-2.40239.33017.49439.75120.28961.14280.64991.1664-0.7082-1.5336-0.8099-0.7298-0.03840.68650.0154-0.1680.39140.03950.4611-29.1206-5.221131.0559
26.4729-2.66093.16153.1716-1.15734.4279-0.8999-0.31570.2667-1.03541.42380.7788-0.1319-1.1021-0.34840.6601-0.0595-0.18030.53470.09110.6542-23.5739-6.694411.3386
33.8132-2.4814-3.27758.091-0.41613.6951-0.69250.1562-0.1845-1.47920.42050.34120.17570.61390.2860.8002-0.0391-0.22290.593-0.00660.5575-27.2137-13.91825.0155
49.33441.4853-2.51698.5055-4.4914.01010.10880.34592.1839-0.2920.28962.7486-0.0591-0.7749-0.34240.54860.0379-0.00870.68650.0161.0127-34.5534-4.533512.3384
55.6895.61937.25065.72837.17779.2396-0.7848-0.6053-0.2975-1.66690.02250.2471-1.2579-0.46020.55880.65180.0311-0.09990.6324-0.10050.7851-27.7856-8.617717.274
64.645-5.57360.14496.98550.66978.7096-1.61480.57130.14851.82890.4904-0.3049-0.03170.24680.64290.6521-0.1370.02780.45-0.03430.4619-2.7246-3.9698-8.0818
75.8427-1.36723.22539.1378-4.89017.0992-0.2965-0.24950.171-0.23850.092-0.53260.3978-0.66850.15340.53050.06010.06220.52480.01680.4269-4.41423.372111.4298
84.08033.1596-4.37344.0667-1.72816.84630.7885-2.2152-0.5270.385-0.7227-0.065-0.4840.22530.09970.53050.0546-0.00080.86960.06180.5005-10.4909-1.545717.8052
98.94615.70161.96037.78961.15278.30230.18510.0661-3.1127-0.0844-0.3955-1.08471.60711.3350.28820.80920.2578-0.12590.7316-0.10561.06630.4164-6.976410.9405
102.071-1.8449-3.48964.8078-1.57321.5528-0.9592-0.0049-0.9679-1.29050.57450.0492-1.24751.029-0.36051.1427-0.17350.10631.0968-0.20220.5507-6.9491-3.0655.7323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 16 )A7 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 32 )A17 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 49 )A33 - 49
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 68 )A50 - 68
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 79 )A72 - 79
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 16 )B7 - 16
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 32 )B17 - 32
8X-RAY DIFFRACTION8chain 'B' and (resid 33 through 49 )B33 - 49
9X-RAY DIFFRACTION9chain 'B' and (resid 50 through 68 )B50 - 68
10X-RAY DIFFRACTION10chain 'B' and (resid 73 through 79 )B73 - 79

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