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- PDB-5tee: Crystal structure of Gemin5 WD40 repeats in apo form -

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Basic information

Entry
Database: PDB / ID: 5tee
TitleCrystal structure of Gemin5 WD40 repeats in apo form
ComponentsGem-associated protein 5
KeywordsSPLICING / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


SMN-Gemin2 complex / Gemini of Cajal 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 Cajal 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 / regulation of translation / ribosome binding / snRNP Assembly / protein-containing complex assembly / SARS-CoV-2 modulates host translation machinery / nuclear body / translation / RNA binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / : / : / : / : / RIG first beta-propeller / GEMI5 TPR domain / RIG second beta-propeller / GEMI5 RBS C-terminal domain / Anaphase-promoting complex subunit 4 WD40 domain ...: / : / : / : / : / RIG first beta-propeller / GEMI5 TPR domain / RIG second beta-propeller / GEMI5 RBS C-terminal 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. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Gem-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsChao, X. / Tempel, W. / Bian, C. / Cerovina, T. / He, H. / Walker, J.R. / Seitova, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Chao, X. / Tempel, W. / Bian, C. / Cerovina, T. / He, H. / Walker, J.R. / 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 21, 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 / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gem-associated protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,49241
Polymers84,1701
Non-polymers32240
Water7,566420
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-20 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.811, 124.407, 61.034
Angle α, β, γ (deg.)90.000, 119.490, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAuthors did not provide a 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) / Strain (production host): SF9 / References: UniProt: Q8TEQ6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 35 / Source method: obtained synthetically
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 15% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.65→48.71 Å / Num. obs: 93484 / % possible obs: 98.9 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.054 / Rrim(I) all: 0.107 / Net I/σ(I): 10.8 / Num. measured all: 355460
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.683.81.0151.31724945010.4950.5991.17997.8
9.04-48.713.60.03335.921375890.9970.020.03997.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FFAS03/SCWRL models based on PDB entries 3ow8, 2hes, 3dm0

3ow8

2hes

3dm0


Resolution: 1.65→48.47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.992 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085
Details: Molecular replacement search models were based on PDB entries 3ow8, 2hes, 3dm0 and modified using SCWRL and the FFAS03 server. Programs Phaser and Molrep were used for molecular replacement. ...Details: Molecular replacement search models were based on PDB entries 3ow8, 2hes, 3dm0 and modified using SCWRL and the FFAS03 server. Programs Phaser and Molrep were used for molecular replacement. Arp/warp was used for map imrpovement and automated model building. Geometry restraints for the ligand were prepared with PRODRG based on GTG coordinates from PDB entry 3HXI. Coot was used for interactive model building. PHENIX.molprobity was used for geometry validation.
RfactorNum. reflection% reflection
Rfree0.1945 4684 5 %
Rwork0.1635 --
obs0.165 88765 98.76 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.85 Å2 / Biso mean: 21.435 Å2 / Biso min: 10.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20.63 Å2
2---0.6 Å20 Å2
3----0.33 Å2
Refinement stepCycle: final / Resolution: 1.65→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 55 420 5773
Biso mean--28.56 28.31 -
Num. residues----691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195706
X-RAY DIFFRACTIONr_bond_other_d0.0030.025214
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9367834
X-RAY DIFFRACTIONr_angle_other_deg0.972312065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54923.745243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66415889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5451529
X-RAY DIFFRACTIONr_chiral_restr0.10.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216547
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021341
X-RAY DIFFRACTIONr_mcbond_it2.2662.0432838
X-RAY DIFFRACTIONr_mcbond_other2.2442.0422837
X-RAY DIFFRACTIONr_mcangle_it3.3313.0483565
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 330 -
Rwork0.281 6483 -
all-6813 -
obs--97.9 %

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