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- PDB-6rnq: Crystal structure of the dimerization domain of Gemin5 at 1.95 A -

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Basic information

Entry
Database: PDB / ID: 6rnq
TitleCrystal structure of the dimerization domain of Gemin5 at 1.95 A
ComponentsGem-associated protein 5
KeywordsRNA BINDING PROTEIN / Dimerization / translation / Tetratricopeptide repeat (TPR) / SMN complex
Function / homology
Function and homology information


SMN-Gemin2 complex / Gemini of coiled bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / U4 snRNA binding / SMN-Sm protein complex / spliceosomal snRNP assembly / U1 snRNA binding ...SMN-Gemin2 complex / Gemini of coiled bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / U4 snRNA binding / SMN-Sm protein complex / spliceosomal snRNP assembly / U1 snRNA binding / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / ribosome binding / regulation of translation / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / protein-containing complex assembly / nuclear body / translation / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / MIOS, WD40 repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...: / MIOS, WD40 repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / Gem-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsMoreno-Morcillo, M. / Ramon-Maiques, S. / Martinez-Salas, E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU-2016-80570-R; AEI/FEDER, UE Spain
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural basis for the dimerization of Gemin5 and its role in protein recruitment and translation control.
Authors: Moreno-Morcillo, M. / Francisco-Velilla, R. / Embarc-Buh, A. / Fernandez-Chamorro, J. / Ramon-Maiques, S. / Martinez-Salas, E.
History
DepositionMay 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gem-associated protein 5
B: Gem-associated protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0453
Polymers56,0062
Non-polymers391
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS analysis: the protein construct elutes as a dimer of approximately 64 kDa in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-49 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.219, 54.972, 103.640
Angle α, β, γ (deg.)90.000, 104.300, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Gem-associated protein 5 / Gemin5


Mass: 28003.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 Rosetta(DE3)pLys / References: UniProt: Q8TEQ6
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 3.27 Å3/Da / Density % sol: 62.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM NaK Tartrate, 25% PEG 3350 and 100 mM BisTris Methane pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→100.4 Å / Num. obs: 51558 / % possible obs: 99.17 % / Redundancy: 3.4 % / Biso Wilson estimate: 41.1 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.96
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 5087

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
AutoSol1.13_2998phasing
XDSdata reduction
Aimlessdata scaling
autoPROCdata scaling
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→100.4 Å / SU ML: 0.3094 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.4181
RfactorNum. reflection% reflection
Rfree0.2354 2539 4.96 %
Rwork0.2106 --
obs0.2118 51194 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.57 Å2
Refinement stepCycle: LAST / Resolution: 1.95→100.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3819 0 1 74 3894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01163895
X-RAY DIFFRACTIONf_angle_d0.87415272
X-RAY DIFFRACTIONf_chiral_restr0.0451598
X-RAY DIFFRACTIONf_plane_restr0.0057669
X-RAY DIFFRACTIONf_dihedral_angle_d18.1442327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.53511400.51492645X-RAY DIFFRACTION99.22
1.98-2.020.47391400.46472723X-RAY DIFFRACTION99.24
2.02-2.070.42611510.41042673X-RAY DIFFRACTION99.47
2.07-2.120.38121390.35012693X-RAY DIFFRACTION99.23
2.12-2.170.31861340.30222677X-RAY DIFFRACTION99.19
2.17-2.230.2811360.27622711X-RAY DIFFRACTION99.75
2.23-2.290.25341180.26492729X-RAY DIFFRACTION98.92
2.29-2.370.27361360.23762672X-RAY DIFFRACTION99.43
2.37-2.450.26991490.22172673X-RAY DIFFRACTION99.26
2.45-2.550.26531740.2272681X-RAY DIFFRACTION99.13
2.55-2.670.27921450.22932690X-RAY DIFFRACTION99.37
2.67-2.810.22351260.21442723X-RAY DIFFRACTION99.37
2.81-2.980.24281150.2212718X-RAY DIFFRACTION99.58
2.98-3.210.30051650.23092711X-RAY DIFFRACTION99.17
3.21-3.540.22981530.20662684X-RAY DIFFRACTION98.82
3.54-4.050.2091510.18122709X-RAY DIFFRACTION98.96
4.05-5.10.1751400.1572725X-RAY DIFFRACTION98.59
5.1-100.560.17431270.16912818X-RAY DIFFRACTION98.53

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