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- PDB-5h1m: Crystal structure of WD40 repeat domains of Gemin5 in complex with M7G -

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Basic information

Entry
Database: PDB / ID: 5h1m
TitleCrystal structure of WD40 repeat domains of Gemin5 in complex with M7G
ComponentsGem-associated protein 5
KeywordsSPLICING / WD repeat / Gemin5 / SMN
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
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / Gem-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.492 Å
AuthorsJin, W. / Wang, Y. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8872
Polymers81,4281
Non-polymers4591
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-3 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.534, 120.907, 61.257
Angle α, β, γ (deg.)90.000, 117.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gem-associated protein 5 / Gemin5


Mass: 81428.109 Da / Num. of mol.: 1 / 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: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 459.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N5O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES (pH 7.5), 14% PEG 8000, 25mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26965 / % possible obs: 99.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 64.24 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Rrim(I) all: 0.084 / Χ2: 1.035 / Net I/av σ(I): 15.937 / Net I/σ(I): 11.2 / Num. measured all: 89686
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.593.30.60926800.6880.3870.7230.9499.6
2.59-2.693.30.49226800.8050.3170.5871.12299.3
2.69-2.823.30.33527240.8810.2140.3981.04399.6
2.82-2.963.30.22226840.9410.1410.2631.05199.3
2.96-3.153.30.15427020.9670.0980.1831.03599.4
3.15-3.393.30.10527190.9820.0670.1251.02799.4
3.39-3.733.30.08626770.9860.0560.1021.03999
3.73-4.273.30.0726950.990.0450.0841.02799.3
4.27-5.383.30.05827110.9920.0380.0690.97699.2
5.38-503.40.0426930.9960.0260.0471.08896.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H1J

5h1j


Resolution: 2.492→29.341 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 1401 5.2 %Random selection
Rwork0.1822 25535 --
obs0.1849 26936 98.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.91 Å2 / Biso mean: 70.8732 Å2 / Biso min: 35.56 Å2
Refinement stepCycle: final / Resolution: 2.492→29.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5309 0 29 33 5371
Biso mean--86.51 58.48 -
Num. residues----674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035509
X-RAY DIFFRACTIONf_angle_d0.6697513
X-RAY DIFFRACTIONf_chiral_restr0.026821
X-RAY DIFFRACTIONf_plane_restr0.003948
X-RAY DIFFRACTIONf_dihedral_angle_d11.6631961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4918-2.58080.29481400.23912387252793
2.5808-2.68410.3051620.25982555271799
2.6841-2.80610.32571270.248525922719100
2.8061-2.95390.30541240.24842585270999
2.9539-3.13880.31421370.22752558269599
3.1388-3.38090.30451310.21152611274299
3.3809-3.72050.23851490.19362541269099
3.7205-4.25740.20621450.17212564270999
4.2574-5.35860.16591580.13682558271699
5.3586-29.34330.23891280.16332584271297

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