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- PDB-8oik: D-PHAT domain (NTD) of human SAMD4A -

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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 / synapse / dendrite / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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