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- PDB-5h1k: Crystal structure of WD40 repeat domains of Gemin5 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5h1k
TitleCrystal structure of WD40 repeat domains of Gemin5 in complex with 13-nt U4 snRNA fragment
Components
  • Gem-associated protein 5
  • U4 snRNA (5'-R(*GP*CP*AP*AP*UP*UP*UP*UP*UP*GP*AP*CP*A)-3')
KeywordsSPLICING/RNA / WD repeat / Gemin5 / SMN / RNA binding / U4 snRNA / SPLICING-RNA complex
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 / Quinoprotein alcohol dehydrogenase-like superfamily ...: / : / : / : / : / RIG first beta-propeller / GEMI5 TPR domain / RIG second beta-propeller / GEMI5 RBS C-terminal 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
: / RNA / RNA (> 10) / Gem-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, Y. / Jin, W. / Liu, C.P. / Yang, N. / Jin, M. / Cong, Y. / Wang, M. / Xu, R.M.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570747 China
National Natural Science Foundation of China31622020 China
National Natural Science Foundation of China31430018 China
National Natural Science Foundation of China31521002 China
Beijing Natural Science Foundation5164038 China
Strategic Priority Research Program of Chinese Academy of SciencesXDB08010100 China
CitationJournal: Genes Dev. / Year: 2016
Title: Structural basis for snRNA recognition by the double-WD40 repeat domain of Gemin5
Authors: Jin, W. / Wang, Y. / Liu, C.P. / Yang, N. / Jin, M. / Cong, Y. / Wang, M. / Xu, R.M.
History
DepositionOct 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: U4 snRNA (5'-R(*GP*CP*AP*AP*UP*UP*UP*UP*UP*GP*AP*CP*A)-3')
D: U4 snRNA (5'-R(*GP*CP*AP*AP*UP*UP*UP*UP*UP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)171,0634
Polymers171,0634
Non-polymers00
Water23,9601330
1
A: Gem-associated protein 5
C: U4 snRNA (5'-R(*GP*CP*AP*AP*UP*UP*UP*UP*UP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)85,5322
Polymers85,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-16 kcal/mol
Surface area27240 Å2
MethodPISA
2
B: Gem-associated protein 5
D: U4 snRNA (5'-R(*GP*CP*AP*AP*UP*UP*UP*UP*UP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)85,5322
Polymers85,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-18 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.654, 107.191, 151.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gem-associated protein 5 / Gemin5


Mass: 81428.109 Da / Num. of mol.: 2 / Fragment: UNP residues 1-726
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Plasmid: pFastBac-HTC / Cell (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEQ6
#2: RNA chain U4 snRNA (5'-R(*GP*CP*AP*AP*UP*UP*UP*UP*UP*GP*AP*CP*A)-3')


Mass: 4103.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: NR_003925
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1330 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4% Tacsimate (pH 8.0), 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 126392 / % possible obs: 99.7 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 17.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.8 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H1J

5h1j


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.968 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.131 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20626 6307 5 %RANDOM
Rwork0.17033 ---
obs0.17216 119452 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10694 522 0 1330 12546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911839
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.91116304
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32551447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56223.665483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.478151825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6551556
X-RAY DIFFRACTIONr_chiral_restr0.0870.21794
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218854
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 398 -
Rwork0.242 8015 -
obs--93.96 %

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