[English] 日本語
Yorodumi
- PDB-5ljm: Structure of SPATA2 PUB domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ljm
TitleStructure of SPATA2 PUB domain
ComponentsSpermatogenesis-associated protein 2
KeywordsCELL CYCLE / PUB domain
Function / homology
Function and homology information


protein linear deubiquitination / regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / protein K63-linked deubiquitination / TNFR1-induced proapoptotic signaling / seminiferous tubule development / ubiquitin-specific protease binding / necroptotic process / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling ...protein linear deubiquitination / regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / protein K63-linked deubiquitination / TNFR1-induced proapoptotic signaling / seminiferous tubule development / ubiquitin-specific protease binding / necroptotic process / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / fibrillar center / signaling receptor complex adaptor activity / regulation of inflammatory response / spermatogenesis / protein-containing complex binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spermatogenesis-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.454 Å
AuthorsElliott, P.R. / Komander, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Mol.Cell / Year: 2016
Title: SPATA2 Links CYLD to LUBAC, Activates CYLD, and Controls LUBAC Signaling.
Authors: Elliott, P.R. / Leske, D. / Hrdinka, M. / Bagola, K. / Fiil, B.K. / McLaughlin, S.H. / Wagstaff, J. / Volkmar, N. / Christianson, J.C. / Kessler, B.M. / Freund, S.M. / Komander, D. / Gyrd-Hansen, M.
History
DepositionJul 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1May 1, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spermatogenesis-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0363
Polymers24,8511
Non-polymers1842
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-0 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.480, 51.140, 56.290
Angle α, β, γ (deg.)90.000, 105.970, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Spermatogenesis-associated protein 2 / Spermatogenesis-associated protein PD1


Mass: 24851.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPATA2, KIAA0757, PD1 / Plasmid: pOPINK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta II / References: UniProt: Q9UM82
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6
Details: Crystals grew at 277K over two weeks in: 20 mM MES pH 6.0, 200 mM NaCl, 4 mM DTT

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.45→54.12 Å / Num. obs: 37750 / % possible obs: 90.2 % / Redundancy: 3 % / Biso Wilson estimate: 15.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Net I/av σ(I): 12.1 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.45-1.482.90.3792.20.908181.2
7.97-54.123.30.038380.99199.8

-
Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
DIALSdata reduction
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: idealised helices in AMPLE

Resolution: 1.454→54.117 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.93
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1877 5.01 %Random selection
Rwork0.1822 ---
obs0.1843 37458 89.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.81 Å2 / Biso mean: 27.1847 Å2 / Biso min: 14.48 Å2
Refinement stepCycle: final / Resolution: 1.454→54.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 12 308 1959
Biso mean--21.75 38.05 -
Num. residues----203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051779
X-RAY DIFFRACTIONf_angle_d0.7722413
X-RAY DIFFRACTIONf_chiral_restr0.066268
X-RAY DIFFRACTIONf_plane_restr0.005307
X-RAY DIFFRACTIONf_dihedral_angle_d21.995700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4542-1.49360.31381110.29882311242276
1.4936-1.53750.30781420.24162343248579
1.5375-1.58710.24411550.21843040319599
1.5871-1.64390.24361580.20733017317599
1.6439-1.70970.21581900.18962961315199
1.7097-1.78750.22631450.1863017316299
1.7875-1.88180.25471680.19793028319699
1.8818-1.99970.2615780.2131601167952
1.9997-2.15410.21931470.17742708285589
2.1541-2.37080.26261250.19842654277987
2.3708-2.71390.19941450.16712933307894
2.7139-3.41910.2251410.172830843225100
3.4191-54.15480.20341720.16482884305692

+
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