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- PDB-5vsx: Structure of the Ubl domain of Sacsin -

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Basic information

Entry
Database: PDB / ID: 5vsx
TitleStructure of the Ubl domain of Sacsin
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 ...: / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 13, 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
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)19,7372
Polymers19,7372
Non-polymers00
Water1,06359
1
A: Sacsin


Theoretical massNumber of molelcules
Total (without water)9,8681
Polymers9,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sacsin


Theoretical massNumber of molelcules
Total (without water)9,8681
Polymers9,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.901, 62.606, 90.834
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: 9868.347 Da / Num. of mol.: 2 / Fragment: Ubl domain (UNP residues 2-85)
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


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.87 Å3/Da / Density % sol: 34.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 0.1 M Bicine pH 8.7, 0.2 M NaCl, 20% sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 8861 / % possible obs: 98.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.06 / Χ2: 0.989 / Net I/σ(I): 20.7 / Num. measured all: 92223
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.1-2.148.10.2890.917182.1
2.14-2.189.10.2720.892197.3
2.18-2.2210.40.260.9011100
2.22-2.2610.30.2410.9391100
2.26-2.3110.80.1960.9941100
2.31-2.3710.50.1811.0531100
2.37-2.4210.60.1531.0791100
2.42-2.4910.90.1431.0841100
2.49-2.5610.50.1291.0681100
2.56-2.6510.80.1030.9981100
2.65-2.7410.70.0951.0811100
2.74-2.8510.70.0860.9691100
2.85-2.9810.70.0750.981100
2.98-3.1410.70.0691.0121100
3.14-3.3310.80.0611.0311100
3.33-3.5910.80.0550.9411100
3.59-3.9510.60.0490.9681100
3.95-4.5210.50.0440.941100
4.52-5.710.50.0450.881100
5.7-509.70.0421.009196.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VSZ, SeMet-L78M mutant

5vsz


Resolution: 2.1→25.951 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.99
RfactorNum. reflection% reflection
Rfree0.2473 421 4.76 %
Rwork0.1866 --
obs0.1895 8842 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.97 Å2 / Biso mean: 41.168 Å2 / Biso min: 18.65 Å2
Refinement stepCycle: final / Resolution: 2.1→25.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 0 59 1234
Biso mean---45.22 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111269
X-RAY DIFFRACTIONf_angle_d1.271730
X-RAY DIFFRACTIONf_chiral_restr0.051191
X-RAY DIFFRACTIONf_plane_restr0.006216
X-RAY DIFFRACTIONf_dihedral_angle_d14.6456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0997-2.40340.28921290.20092711284097
2.4034-3.02730.30911460.224227982944100
3.0273-25.95250.21711460.169729123058100
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)
16.0249-0.5591-0.12395.15111.26724.40480.2620.4752-0.51410.4304-0.26730.1150.61120.0173-0.04150.22660.02120.01570.2177-0.0570.302729.18923.562231.7676
23.3458-0.6979-0.24336.00143.50864.81320.06880.27380.0955-0.29640.06270.0584-0.54740.0008-0.1130.25260.00080.03990.16880.03860.229723.60677.658410.7383
32.4649-1.27461.02117.48430.7595.1116-0.1070.01910.0654-0.5419-0.12450.04780.1129-0.29130.19590.2235-0.01250.02590.24730.02240.192827.019314.30734.9527
43.47731.3306-0.61886.04860.54835.29650.0251-0.0609-0.88620.0142-0.3351-0.89310.54010.97370.24080.25580.07020.010.31710.08480.377135.32185.080411.4163
57.72061.2325-1.99578.4504-1.02417.5998-0.05640.1301-1.12080.8168-0.0055-0.75540.85980.385-0.02790.36820.034-0.08090.2898-0.00390.291627.68825.772917.5007
65.5185-3.5108-2.59767.3358-0.25731.8327-0.6069-0.1545-0.6570.36230.68080.5815-0.1828-0.2971-0.10020.2309-0.02020.04730.1685-0.0110.23890.44034.4101-9.212
75.38250.0092-4.24321.1684-0.6393.89840.1169-0.55150.13530.05730.0225-0.0044-0.1690.5294-0.12980.2885-0.0162-0.0030.3178-0.02830.16844.325-3.028811.9183
89.3406-1.60871.18134.23730.36315.60380.2876-1.0432-0.13050.61290.0795-0.00330.35590.2433-0.32610.30030.0216-0.00490.29290.00840.127210.27521.455217.685
97.11180.3994-0.58662.1135-1.11174.2303-0.03940.13981.8070.43450.31250.6796-0.7555-0.7512-0.1380.38970.07950.10670.31270.01950.4404-0.01697.769110.9174
105.9944-1.66830.35684.18851.89765.4508-0.20111.22470.0729-0.14840.38420.7459-0.0261-0.3341-0.25210.31240.01340.03120.49040.15460.30682.7711.35554.8579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 16 )A6 - 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 66 )A50 - 66
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 79 )A67 - 79
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 16 )B5 - 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 66 )B50 - 66
10X-RAY DIFFRACTION10chain 'B' and (resid 67 through 79 )B67 - 79

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