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- PDB-5tha: Gemin5 WD40 repeats in complex with a guanosyl moiety -

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Basic information

Entry
Database: PDB / ID: 5tha
TitleGemin5 WD40 repeats in complex with a guanosyl moiety
ComponentsGem-associated protein 5
KeywordsRNA BINDING PROTEIN / WD40 repeat / Structural Genomics / Structural Genomics Consortium / SGC
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 / SMN-Sm protein complex / U4 snRNA binding / 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 / SMN-Sm protein complex / U4 snRNA binding / 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 / cytoplasm / cytosol
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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...MIOS, WD40 repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Mainly Beta
Similarity search - Domain/homology
DIGUANOSINE-5'-TRIPHOSPHATE / Gem-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsChao, X. / Tempel, W. / Bian, C. / Cerovina, T. / He, H. / Seitova, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Genes Dev. / Year: 2016
Title: Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly.
Authors: Xu, C. / Ishikawa, H. / Izumikawa, K. / Li, L. / He, H. / Nobe, Y. / Yamauchi, Y. / Shahjee, H.M. / Wu, X.H. / Yu, Y.T. / Isobe, T. / Takahashi, N. / Min, J.
History
DepositionSep 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2May 10, 2017Group: Structure summary
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gem-associated protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,95923
Polymers84,1701
Non-polymers78822
Water5,567309
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-2 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.198, 125.253, 60.889
Angle α, β, γ (deg.)90.000, 117.100, 90.000
Int Tables number4
Space group name H-MP1211
Detailsauthors did not provide biological assembly

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Components

#1: Protein Gem-associated protein 5 / Gemin5


Mass: 84170.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Plasmid: pFBOH-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEQ6
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 21 / Source method: obtained synthetically
#3: Chemical ChemComp-GP3 / DIGUANOSINE-5'-TRIPHOSPHATE


Mass: 788.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N10O18P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na-Citrate, pH 5.5, 0.2 M Ammonium Acetate, and 18% PEG4K with 1 mM GpppG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→32.51 Å / Num. obs: 69342 / % possible obs: 96.8 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Net I/σ(I): 17.9 / Num. measured all: 260153
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.840.5962.21420839090.7840.3580.69691.5
9-32.510.0166421195870.9990.010.01997.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→32.51 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.544 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.109
Details: An isomorphous crystal structure was used as the starting model. Coot was used for interactive model building. GP3 geometry restraints were prepared on the GRADE server. Only one guanosyl ...Details: An isomorphous crystal structure was used as the starting model. Coot was used for interactive model building. GP3 geometry restraints were prepared on the GRADE server. Only one guanosyl moiety of GP3 was resolved in the electron density map. Phenix was used for the calculation of some omit difference maps. PHENIX.molprobity was used for geometry validation.
RfactorNum. reflection% reflection
Rfree0.2004 3486 5 %
Rwork0.167 --
obs0.1687 65819 96.59 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.39 Å2 / Biso mean: 24.638 Å2 / Biso min: 12.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20.09 Å2
2---1.5 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.8→32.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5204 0 45 309 5558
Biso mean--29.31 28.9 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195519
X-RAY DIFFRACTIONr_bond_other_d0.0030.025002
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9347565
X-RAY DIFFRACTIONr_angle_other_deg0.948311555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.745714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88923.911225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9115841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1861522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216318
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021274
X-RAY DIFFRACTIONr_mcbond_it2.4522.4512762
X-RAY DIFFRACTIONr_mcbond_other2.4512.452761
X-RAY DIFFRACTIONr_mcangle_it3.5213.6513454
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 235 -
Rwork0.257 4628 -
all-4863 -
obs--92.12 %

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