[English] 日本語
Yorodumi
- PDB-3emw: Crystal Structure of human splA/ryanodine receptor domain and SOC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3emw
TitleCrystal Structure of human splA/ryanodine receptor domain and SOCS box containing 2 (SPSB2) in complex with a 20-residue VASA peptide
Components
  • Peptide (VASA)
  • SPRY domain-containing SOCS box protein 2
KeywordsAPOPTOSIS / Apoptosis nucleus / UBL conjugation pathwayc / CL transcription regulation / Transcription / Phosphoprotein / Ubl conjugation pathway / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


secondary piRNA processing / posterior cell cortex / gamete generation / P granule / germ cell nucleus / SCF ubiquitin ligase complex / oogenesis / germ cell development / ubiquitin-like ligase-substrate adaptor activity / protein localization ...secondary piRNA processing / posterior cell cortex / gamete generation / P granule / germ cell nucleus / SCF ubiquitin ligase complex / oogenesis / germ cell development / ubiquitin-like ligase-substrate adaptor activity / protein localization / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA helicase activity / cell differentiation / intracellular signal transduction / protein ubiquitination / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ded1/Dbp1, DEAD-box helicase domain / SSB2, SOCS box domain / : / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / DEAD-box subfamily ATP-dependent helicases signature. ...Ded1/Dbp1, DEAD-box helicase domain / SSB2, SOCS box domain / : / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Concanavalin A-like lectin/glucanase domain superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent RNA helicase vasa / SPRY domain-containing SOCS box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFilippakopoulos, P. / Sharpe, T. / Keates, T. / Murray, J.W. / Savitsky, P. / Roos, A.K. / Pike, A.C.W. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Filippakopoulos, P. / Sharpe, T. / Keates, T. / Murray, J.W. / Savitsky, P. / Roos, A.K. / Pike, A.C.W. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural basis for Par-4 recognition by the SPRY domain- and SOCS box-containing proteins SPSB1, SPSB2, and SPSB4.
Authors: Filippakopoulos, P. / Low, A. / Sharpe, T.D. / Uppenberg, J. / Yao, S. / Kuang, Z. / Savitsky, P. / Lewis, R.S. / Nicholson, S.E. / Norton, R.S. / Bullock, A.N.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SPRY domain-containing SOCS box protein 2
B: Peptide (VASA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5966
Polymers26,3472
Non-polymers2484
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint6.5 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.470, 61.963, 118.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SPRY domain-containing SOCS box protein 2 / SPSB2 / SSB-2 / Gene-rich cluster protein C9


Mass: 23849.627 Da / Num. of mol.: 1 / Fragment: UNP residues 26-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB2, GRCC9, SSB2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q99619
#2: Protein/peptide Peptide (VASA)


Mass: 2497.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: P09052*PLUS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.178M Na/KPO4, 17.8% PEG3350, 8.88% EtGly, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.975653 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975653 Å / Relative weight: 1
ReflectionResolution: 1.8→42.83 Å / Num. obs: 24366 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.22 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3494 / Rsym value: 0.618 / % possible all: 100

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JK9

2jk9


Resolution: 1.8→42.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.491 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21593 1239 5.1 %RANDOM
Rwork0.17796 ---
all0.17995 23115 --
obs0.17995 23073 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.523 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2--0.97 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 16 138 1733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211636
X-RAY DIFFRACTIONr_bond_other_d0.0020.021130
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9632217
X-RAY DIFFRACTIONr_angle_other_deg0.95332732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3223.37874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81615245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.461513
X-RAY DIFFRACTIONr_chiral_restr0.0920.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_mcbond_it3.34831022
X-RAY DIFFRACTIONr_mcbond_other1.1743426
X-RAY DIFFRACTIONr_mcangle_it4.47951621
X-RAY DIFFRACTIONr_scbond_it6.898614
X-RAY DIFFRACTIONr_scangle_it8.46511596
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 87 -
Rwork0.233 1665 -
obs--99.94 %
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)
13.301-2.3859-3.970811.4412-0.07516.9983-0.1075-0.13820.25970.2783-0.0075-0.6335-0.09471.01430.1150.1238-0.0202-0.01780.1489-0.070.21224.31337.260731.4895
21.82770.52970.292.24870.36781.83070.0645-0.08570.0606-0.12830.04720.0815-0.1639-0.1821-0.1117-0.0175-0.003-0.00070.00180.03410.00849.266524.329842.0027
32.1064-0.0929-0.14421.8770.17151.96110.0445-0.1437-0.29060.04370.0779-0.04040.1755-0.0389-0.1224-0.0117-0.028-0.0419-0.01760.03670.031814.74513.783843.9152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 32
2X-RAY DIFFRACTION2A33 - 121
3X-RAY DIFFRACTION3A122 - 219

+
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