[English] 日本語
Yorodumi
- PDB-8oik: D-PHAT domain (NTD) of human SAMD4A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oik
TitleD-PHAT domain (NTD) of human SAMD4A
ComponentsProtein Smaug homolog 1
KeywordsRNA BINDING PROTEIN / protein interaction domain / dimerization domain
Function / homology
Function and homology information


nuclear-transcribed mRNA poly(A) tail shortening / translation repressor activity / positive regulation of translation / P-body / fibrillar center / cell junction / mRNA binding / dendrite / synapse / RNA binding / cytosol
Similarity search - Function
Smaug, PHAT domain superfamily / Protein Smaug, SAM domain / : / SAM domain (Sterile alpha motif) / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein Smaug homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.62 Å
AuthorsKubikova, J. / Jeske, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural basis for binding of Drosophila Smaug to the GPCR Smoothened and to the germline inducer Oskar.
Authors: Kubikova, J. / Ubartaite, G. / Metz, J. / Jeske, M.
#1: Journal: bioRxiv / Year: 2023
Title: Structural basis for binding of Smaug to the GPCR Smoothened and to the germline inducer Oskar
Authors: Kubikova, J. / Ubartaite, G. / Metz, J. / Jeske, M.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein Smaug homolog 1
B: Protein Smaug homolog 1
C: Protein Smaug homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8707
Polymers62,4893
Non-polymers3804
Water6,215345
1
A: Protein Smaug homolog 1
C: Protein Smaug homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8724
Polymers41,6602
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein Smaug homolog 1
hetero molecules

B: Protein Smaug homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9966
Polymers41,6602
Non-polymers3364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Unit cell
Length a, b, c (Å)81.829, 142.786, 137.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

21C-392-

HOH

-
Components

#1: Protein Protein Smaug homolog 1 / Smaug 1 / hSmaug1 / Sterile alpha motif domain-containing protein 4A / SAM domain-containing protein 4A


Mass: 20829.803 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMD4A, KIAA1053, SAMD4, SMAUG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UPU9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.6, 8% jeffamine M-600 pH 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.968, 0.98,
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9681
20.981
ReflectionResolution: 1.62→63.05 Å / Num. obs: 89788 / % possible obs: 95.2 % / Redundancy: 13.8 % / Biso Wilson estimate: 33.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.062 / Net I/σ(I): 19.2
Reflection shellResolution: 1.62→1.7 Å / Num. unique obs: 4488 / CC1/2: 0.34

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.62→49.45 Å / SU ML: 0.1639 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2209 2001 2.23 %
Rwork0.207 87723 -
obs0.2073 89724 87.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.14 Å2
Refinement stepCycle: LAST / Resolution: 1.62→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 25 350 4179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793903
X-RAY DIFFRACTIONf_angle_d0.94685283
X-RAY DIFFRACTIONf_chiral_restr0.0547607
X-RAY DIFFRACTIONf_plane_restr0.0073667
X-RAY DIFFRACTIONf_dihedral_angle_d17.31811434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.4626190.4478784X-RAY DIFFRACTION11.11
1.66-1.70.472660.38393148X-RAY DIFFRACTION44.22
1.7-1.750.34321140.33925303X-RAY DIFFRACTION74.5
1.75-1.810.32061530.30236556X-RAY DIFFRACTION92.54
1.81-1.870.29121600.27827136X-RAY DIFFRACTION99.86
1.87-1.950.28881630.26797115X-RAY DIFFRACTION99.86
1.95-2.040.2531600.24697105X-RAY DIFFRACTION99.89
2.04-2.140.24031650.20817131X-RAY DIFFRACTION99.97
2.14-2.280.21181670.2087179X-RAY DIFFRACTION100
2.28-2.450.25491670.21047141X-RAY DIFFRACTION100
2.45-2.70.2281640.21447174X-RAY DIFFRACTION99.95
2.7-3.090.23151660.20557216X-RAY DIFFRACTION100
3.09-3.890.18771660.18317286X-RAY DIFFRACTION100
3.89-49.450.19951710.19377449X-RAY DIFFRACTION99.74

+
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://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