[English] 日本語
Yorodumi
- PDB-3o10: Crystal structure of the HEPN domain from human sacsin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o10
TitleCrystal structure of the HEPN domain from human sacsin
ComponentsSacsin
KeywordsCHAPERONE / all-helical domain / homodimerization
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 / Nucleotidyltransferases domain 2 / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase/HSP90-like ATPase superfamily ...HEPN domain profile. / Higher Eukarytoes and Prokaryotes Nucleotide-binding domain / HEPN domain / HEPN domain / Nucleotidyltransferases domain 2 / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase/HSP90-like ATPase superfamily / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MALONATE ION / Sacsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis of defects in the sacsin HEPN domain responsible for autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS).
Authors: Kozlov, G. / Denisov, A.Y. / Girard, M. / Dicaire, M.J. / Hamlin, J. / McPherson, P.S. / Brais, B. / Gehring, K.
History
DepositionJul 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 30, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,9347
Polymers64,6284
Non-polymers3063
Water7,332407
1
A: Sacsin
B: Sacsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5184
Polymers32,3142
Non-polymers2042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint3 kcal/mol
Surface area12450 Å2
MethodPISA
2
C: Sacsin
D: Sacsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4163
Polymers32,3142
Non-polymers1021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-5 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.581, 72.581, 201.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-86-

HOH

-
Components

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


Mass: 16156.999 Da / Num. of mol.: 4 / Fragment: HEPN domain residues 4440-4579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SACS, KIAA0730 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NZJ4
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7% (w/v) PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 9, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 46702 / Num. obs: 45815 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.9→1.93 Å / % possible all: 86.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→45.86 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.549 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2441 5.1 %RANDOM
Rwork0.184 ---
obs0.186 45815 98.1 %-
all-46702 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 21 407 4810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224506
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.966099
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1445553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61724.037218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74915794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0621537
X-RAY DIFFRACTIONr_chiral_restr0.10.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023433
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22190
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23118
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2345
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8151.52876
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27624474
X-RAY DIFFRACTIONr_scbond_it2.13131870
X-RAY DIFFRACTIONr_scangle_it3.2354.51622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 149 -
Rwork0.182 2955 -
obs--86.97 %
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)
11.35160.17430.08982.0365-1.49233.0241-0.03480.13680.1031-0.0870.09390.0426-0.0799-0.0572-0.05910.0303-0.0139-0.0090.0350.00330.0699-18.618-8.93125.027
23.0428-0.8174-0.76976.9707-1.5925.11440.00140.4851-0.0148-0.4452-0.0714-0.1962-0.02070.11010.07-0.0033-0.01290.0380.0416-0.00370.0538-6.095-6.8718.79
31.50280.1049-0.20642.1430.30391.1822-0.02250.0451-0.0096-0.0802-0.0056-0.07770.02530.00880.0281-0.02250.0079-0.00230.00060.00390.0707-8.109-23.52533.147
40.8895-0.13470.28984.6929-2.3754.0619-0.02720.02190.05150.10250.0164-0.1612-0.3683-0.0280.01070.0098-0.00190.00690.0213-0.01240.0954-10.579-5.39231.065
52.131-0.94290.11953.5311-0.09811.1175-0.02520.0465-0.23850.10730.0047-0.06430.0749-0.01020.02050.019-0.02250.01140.04930.00160.0874-20.416-29.22636.088
63.57790.69520.00294.7021-0.4431.5183-0.0150.3482-0.4009-0.27210.1121-0.21920.08050.1406-0.097-0.0187-0.03220.0131-0.0033-0.0590.0869-26.379-39.73228.736
71.27651.1956-0.88512.7636-1.34151.5226-0.1290.1513-0.0324-0.23350.10240.05330.0798-0.16720.02650.0025-0.0299-0.03150.04380.00890.0076-28.724-18.45722.342
81.3181-0.34680.01944.452-1.31272.2785-0.07690.095-0.04170.29620.00070.05760.0341-0.08340.07620.007-0.030.00710.0638-0.01750.085-31.14-28.72436.278
947.0184-48.98683.582974.3632-30.120130.1238-0.8556-1.5099-1.0097-0.17041.17191.30780.2015-0.6386-0.31640.06090.04610.1170.00550.0844-0.1171-41.572-40.01216.073
100.8814-1.0358-0.31223.3401-2.94015.2621-0.1769-0.0506-0.0558-0.12590.0335-0.01430.54340.0160.14340.0414-0.0698-0.0430.03050.0328-0.033-44.174-30.5232.186
112.7499-1.46693.88364.1491-3.650515.5925-0.00530.0940.0388-0.1559-0.3838-0.02832.11031.06040.38910.29380.14190.080.00920.0055-0.008-39.976-42.625-3.183
121.18651.4794-1.68043.9379-2.60323.2732-0.103-0.1138-0.2825-0.0074-0.0841-0.1250.3881-0.09810.18710.0346-0.0301-0.0529-0.03850.03060.0369-44.112-30.089-7.733
133.08311.4787-2.42481.7708-2.38396.09470.1622-0.2901-0.15170.1562-0.2095-0.0757-0.11820.23640.04730.0243-0.0307-0.06140.06010.0281-0.0052-35.73-13.481-6.787
142.56510.056-1.22752.7872.146611.2765-0.00070.0807-0.1241-0.11380.0599-0.1574-0.18590.9629-0.0591-0.011-0.0956-0.09620.18740.0836-0.089-24.699-8.494-0.439
155.7623.9355-6.938714.0986-2.57958.7645-0.11770.0949-0.2140.775-0.4697-1.3696-0.03630.49530.58740.0181-0.0615-0.15690.0810.1378-0.0067-35.794-26.17811.125
161.88181.9844-2.66523.8927-2.89628.79570.2598-0.25150.00090.3069-0.31270.0405-0.4263-0.13720.0530.0679-0.0587-0.09840.09850.0053-0.0704-37.97-8.2832.987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4439 - 4496
2X-RAY DIFFRACTION2A4497 - 4525
3X-RAY DIFFRACTION3A4526 - 4549
4X-RAY DIFFRACTION4A4550 - 4577
5X-RAY DIFFRACTION5B4439 - 4495
6X-RAY DIFFRACTION6B4496 - 4524
7X-RAY DIFFRACTION7B4525 - 4549
8X-RAY DIFFRACTION8B4550 - 4577
9X-RAY DIFFRACTION9C4442 - 4448
10X-RAY DIFFRACTION10C4449 - 4495
11X-RAY DIFFRACTION11C4496 - 4532
12X-RAY DIFFRACTION12C4533 - 4577
13X-RAY DIFFRACTION13D4440 - 4496
14X-RAY DIFFRACTION14D4497 - 4530
15X-RAY DIFFRACTION15D4531 - 4548
16X-RAY DIFFRACTION16D4549 - 4576

+
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