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- PDB-5v45: Crystal structure of the F270M, K291M, L318M mutant of SR1 domain... -

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Basic information

Entry
Database: PDB / ID: 5v45
TitleCrystal structure of the F270M, K291M, L318M mutant of SR1 domain of human sacsin
ComponentsSacsin
KeywordsCHAPERONE / alpha-beta sandwich / Bergerat fold
Function / homology
Function and homology information


negative regulation of inclusion body assembly / cell body fiber / low-density lipoprotein particle receptor binding / proteasome binding / Hsp70 protein binding / protein folding / protein-folding chaperone binding / axon / dendrite / mitochondrion ...negative regulation of inclusion body assembly / cell body fiber / low-density lipoprotein particle receptor binding / 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 / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsMenade, M. / Kozlov, G. / 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
DepositionMar 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 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 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sacsin
B: Sacsin


Theoretical massNumber of molelcules
Total (without water)57,5632
Polymers57,5632
Non-polymers00
Water3,009167
1
A: Sacsin


Theoretical massNumber of molelcules
Total (without water)28,7821
Polymers28,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sacsin


Theoretical massNumber of molelcules
Total (without water)28,7821
Polymers28,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.679, 41.360, 74.106
Angle α, β, γ (deg.)99.55, 95.26, 107.50
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 28781.553 Da / Num. of mol.: 2 / Fragment: UNP residues 89-336 / Mutation: F270M, K291M, L318M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SACS, KIAA0730 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NZJ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 28% PEG 3350, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 32566 / % possible obs: 96.19 % / Redundancy: 7.9 % / Rsym value: 0.091 / Net I/σ(I): 43.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2240 / Rsym value: 0.456 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.312 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.22404 1961 5.7 %RANDOM
Rwork0.18608 ---
obs0.18826 32566 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.272 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0.15 Å2-0.14 Å2
2---0.62 Å20.08 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.91→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 0 167 3874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023818
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9645189
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212969
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9591.6231888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4972.4242354
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6241.8081930
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.87717.1694758
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.906→1.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 128 -
Rwork0.222 2240 -
obs--89.09 %
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)
16.5711.48664.58390.41470.87673.52930.2626-0.487-0.02560.0001-0.11730.05560.321-0.3355-0.14530.21260.0441-0.05190.246-0.08320.093743.9562-0.845797.8835
21.1938-0.73530.40773.2989-0.12511.3642-0.0309-0.1740.02920.42750.05110.0239-0.0028-0.0265-0.02020.1095-0.01920.0140.14110.00210.077233.4399-10.44977.4195
33.0867-2.1135-1.67526.13292.43883.65320.09960.040.30070.17530.0544-0.3598-0.25690.2418-0.1540.0547-0.01590.00190.15-0.04960.162844.8174-1.541479.7194
41.7516-0.9426-0.17482.65861.05270.87-0.0176-0.2486-0.01280.47840.1227-0.08160.17120.0233-0.1050.1177-0.0097-0.00580.14760.01780.051235.6721-13.400279.3019
52.3581-0.01370.10446.397-0.22131.6129-0.0374-0.0665-0.1705-0.0556-0.07790.16630.0362-0.2010.11530.08010.005-0.00910.1694-0.00230.110625.302-4.426969.1696
63.17021.20530.220214.9315-3.25793.97470.05230.0808-0.1066-0.2045-0.02340.28770.1932-0.2652-0.02890.0567-0.009-0.01060.1721-0.02110.144219.3836-7.509167.7647
70.46811.10430.72995.61174.36344.6728-0.06380.0786-0.0639-0.07480.07230.073-0.18430.0748-0.00850.15450.0316-0.04460.2405-0.02350.079424.7125-20.440622.5404
84.7399-0.02712.72248.2-4.566410.92390.04540.3429-0.1629-0.53960.06470.23570.33120.0921-0.11020.0460.0030.01710.1508-0.01940.132221.519-16.164948.3194
92.7642-0.2529-0.36251.455-0.45852.20420.02550.2318-0.1402-0.1910.1416-0.05910.01560.0031-0.16710.044-0.03550.03860.1427-0.01510.082736.9855-13.517144.1102
101.7866-0.73870.78391.7921-0.06762.08660.10690.2208-0.0444-0.29410.0402-0.1141-0.07390.1055-0.14710.06-0.02130.04430.1544-0.01020.084438.4916-15.672341.7951
1110.67454.212-4.19094.9762-0.9434.02340.17340.17540.4259-0.21990.00480.5437-0.1335-0.4466-0.17820.13840.0431-0.05140.14880.05910.160119.7518-1.998446.7013
124.42791.54470.7613.29810.91581.7730.1199-0.25140.03720.1186-0.13790.0666-0.1746-0.1390.0180.08080.02280.02250.14730.01950.088724.1988-6.521255.5047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 106
2X-RAY DIFFRACTION2A107 - 167
3X-RAY DIFFRACTION3A168 - 194
4X-RAY DIFFRACTION4A195 - 306
5X-RAY DIFFRACTION5A307 - 325
6X-RAY DIFFRACTION6A326 - 335
7X-RAY DIFFRACTION7B84 - 111
8X-RAY DIFFRACTION8B112 - 128
9X-RAY DIFFRACTION9B129 - 173
10X-RAY DIFFRACTION10B174 - 289
11X-RAY DIFFRACTION11B290 - 306
12X-RAY DIFFRACTION12B307 - 335

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