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- PDB-5gxi: Structure of the Gemin5 WD40 domain in complex with AAUUUUUGAG -

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Basic information

Entry
Database: PDB / ID: 5gxi
TitleStructure of the Gemin5 WD40 domain in complex with AAUUUUUGAG
Components
  • Gem-associated protein 5
  • RNA (5'-R(*A*AP*UP*UP*UP*UP*UP*GP*AP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / snRNP assembly / snRNA / Structural Genomics / Structural Genomics Consortium / SGC / RNA BINDING PROTEIN-RNA 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 / 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 / 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 / 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
RNA / Gem-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsXu, C. / He, H. / Li, Y. / Dong, 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 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Oct 17, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector_type
Revision 1.3Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Dec 14, 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
Revision 1.5Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gem-associated protein 5
B: RNA (5'-R(*A*AP*UP*UP*UP*UP*UP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)87,50124
Polymers87,5012
Non-polymers022
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.850, 124.520, 60.600
Angle α, β, γ (deg.)90.00, 116.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gem-associated protein 5 / / Gemin5


Mass: 84337.359 Da / Num. of mol.: 1 / Fragment: UNP residues 1-739 / Mutation: R682Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEQ6
#2: RNA chain RNA (5'-R(*A*AP*UP*UP*UP*UP*UP*GP*AP*G)-3') / U4 (118-127)


Mass: 3163.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 22 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium citrate, 0.2 M ammonium acetate, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→28.92 Å / Num. obs: 65191 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.998 / Net I/σ(I): 14.9
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.592 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OW8,2HES,3DM0

3ow8

2hes

3dm0


Resolution: 1.85→28.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.017 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20738 3294 5.1 %RANDOM
Rwork0.16395 ---
obs0.16614 61867 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.85→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5150 82 23 381 5636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195509
X-RAY DIFFRACTIONr_bond_other_d0.0020.025005
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9237556
X-RAY DIFFRACTIONr_angle_other_deg1.062311552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1875690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10823.728228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91615840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6081525
X-RAY DIFFRACTIONr_chiral_restr0.1190.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021275
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4072.2942695
X-RAY DIFFRACTIONr_mcbond_other2.4022.2932694
X-RAY DIFFRACTIONr_mcangle_it3.5043.4233366
X-RAY DIFFRACTIONr_mcangle_other3.5043.4233367
X-RAY DIFFRACTIONr_scbond_it2.9432.5522814
X-RAY DIFFRACTIONr_scbond_other2.9422.5532815
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3083.7244174
X-RAY DIFFRACTIONr_long_range_B_refined6.23919.3776333
X-RAY DIFFRACTIONr_long_range_B_other6.16319.1066165
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 255 -
Rwork0.255 4531 -
obs--99.73 %

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