[English] 日本語
Yorodumi
- PDB-5v44: Crystal structure of the SR1 domain of human sacsin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v44
TitleCrystal structure of the 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 / MOLECULAR REPLACEMENT / Resolution: 1.56 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 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sacsin
B: Sacsin
C: Sacsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4639
Polymers85,9103
Non-polymers5536
Water7,008389
1
A: Sacsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9134
Polymers28,6371
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sacsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8213
Polymers28,6371
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sacsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7292
Polymers28,6371
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.068, 41.721, 105.892
Angle α, β, γ (deg.)97.86, 95.76, 107.20
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 28636.795 Da / Num. of mol.: 3
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 3350, 0.2 M ammonium acetate, 0.1 M MES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 86247 / % possible obs: 96.25 % / Redundancy: 4.3 % / Rsym value: 0.049 / Net I/σ(I): 34.6
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5846 / Rsym value: 0.449 / % possible all: 87.96

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V45

5v45


Resolution: 1.56→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.229 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.21445 4459 4.9 %RANDOM
Rwork0.18204 ---
obs0.18362 86247 96.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.172 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.18 Å20.1 Å2
2--0.44 Å20.08 Å2
3----1.1 Å2
Refinement stepCycle: 1 / Resolution: 1.56→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5585 0 36 389 6010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.025807
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9617882
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_restr0.0830.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214503
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_it1.0672.1982801
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6953.2883493
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.672.4443006
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.18223.2537677
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: 1.557→1.597 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 304 -
Rwork0.222 5846 -
obs--87.96 %
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)
10.70190.1781-0.01910.49421.21583.40640.0323-0.109-0.06640.1099-0.0493-0.00510.1718-0.06090.0170.15810.0003-0.01240.01870.01170.07467.823410.0305111.6698
21.31670.22610.24482.21350.71631.35310.0721-0.13590.03490.211-0.08370.16030.0049-0.10370.01160.033-0.010.0090.0267-0.01370.03995.114724.3287104.8885
31.0392-0.14230.48450.493-0.33311.30290.0424-0.16040.02160.08080.01010.0575-0.0272-0.162-0.05250.0204-0.00550.00560.0417-0.01670.03981.897225.2028107.1256
40.59590.01320.08450.8054-0.0911.0431-0.0242-0.0604-0.1514-0.05960.0415-0.0580.02380.1647-0.01740.00970.0087-0.00340.048-0.00810.089717.88713.901597.8634
57.88441.8769-4.59511.2657-1.1842.6906-0.041-0.5241-0.37310.0563-0.1699-0.1870.00330.30590.21090.0862-0.03120.02090.08910.05380.075-7.569-3.674354.0388
60.96480.06190.0041.06650.19961.25970.0672-0.10310.01080.1489-0.0370.00480.0333-0.0485-0.03020.032-0.00610.00240.0186-0.00510.02680.12155.486534.8215
71.5356-0.01950.19421.393-0.34911.36990.0415-0.10750.10250.0915-0.01490.0908-0.0697-0.1424-0.02660.03240.00860.00960.0296-0.02090.0503-4.026711.509636.8331
81.5293-0.36150.39242.56930.81241.78630.0202-0.0134-0.0696-0.04380.1534-0.2684-0.00390.2479-0.17370.00910.00940.0140.053-0.00990.080913.8005-0.164931.2238
90.09470.6052-0.32044.6924-3.15962.62330.0264-0.0375-0.0232-0.1046-0.2392-0.27940.28730.0760.21280.0982-0.02990.02230.09480.06270.076116.632633.614651.2368
101.71430.04920.20690.6439-0.27821.787-0.02340.1430.0548-0.09080.0495-0.0087-0.0773-0.0173-0.02610.0341-0.0028-0.00110.0193-0.00490.02698.59423.768172.0266
111.3241-0.0314-0.95020.80410.13111.91380.02740.20570.1197-0.13090.089-0.0211-0.179-0.1401-0.11640.0527-0.0022-0.00380.05180.01440.02813.494526.912969.5654
122.65471.06681.14371.84790.15191.98040.08010.1267-0.3526-0.09020.0599-0.07580.26050.1285-0.140.04270.0151-0.010.0258-0.03290.082518.2112.802776.1433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 128
2X-RAY DIFFRACTION2A129 - 173
3X-RAY DIFFRACTION3A191 - 286
4X-RAY DIFFRACTION4A287 - 335
5X-RAY DIFFRACTION5B88 - 109
6X-RAY DIFFRACTION6B110 - 194
7X-RAY DIFFRACTION7B195 - 288
8X-RAY DIFFRACTION8B289 - 335
9X-RAY DIFFRACTION9C84 - 110
10X-RAY DIFFRACTION10C111 - 174
11X-RAY DIFFRACTION11C175 - 286
12X-RAY DIFFRACTION12C287 - 336

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more