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- PDB-7bbl: Structure of human Gemin6/Gemin7/Gemin8 trimeric complex -

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Basic information

Entry
Database: PDB / ID: 7bbl
TitleStructure of human Gemin6/Gemin7/Gemin8 trimeric complex
Components
  • Gem-associated protein 6
  • Gem-associated protein 7
  • Gem-associated protein 8
KeywordsSPLICING / UsnRNP / Biogenesis / SMN-complex / Gemin8
Function / homology
Function and homology information


Sm-like protein family complex / Gemini of Cajal bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / nuclear body ...Sm-like protein family complex / Gemini of Cajal bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / nuclear body / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Gemini of Cajal bodies-associated protein 8 / Gemini of Cajal bodies-associated protein 8 / Gem-associated protein 6 / SMN complex, gem-associated protein 7 / Gem-associated protein 6, C-terminal domain / Gem-associated protein 6, Sm-like domain / : / Gemin6 Sm-like domain / Gem-associated protein 7 (Gemin7) / Gemin6 C-terminal domain ...Gemini of Cajal bodies-associated protein 8 / Gemini of Cajal bodies-associated protein 8 / Gem-associated protein 6 / SMN complex, gem-associated protein 7 / Gem-associated protein 6, C-terminal domain / Gem-associated protein 6, Sm-like domain / : / Gemin6 Sm-like domain / Gem-associated protein 7 (Gemin7) / Gemin6 C-terminal domain / AD domain profile. / SUZ-C domain / SUZ-C domain profile. / : / Sm domain profile.
Similarity search - Domain/homology
Gem-associated protein 6 / Gem-associated protein 7 / Gem-associated protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.521 Å
AuthorsViswanathan, A. / Grimm, C. / Fischer, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Fi573/7-2 and 8-2 Germany
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Identification and structural analysis of the Schizosaccharomyces pombe SMN complex.
Authors: Veepaschit, J. / Viswanathan, A. / Bordonne, R. / Grimm, C. / Fischer, U.
History
DepositionDec 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.2Jul 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: 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 6
C: Gem-associated protein 6
D: Gem-associated protein 7
E: Gem-associated protein 8
B: Gem-associated protein 7
F: Gem-associated protein 8


Theoretical massNumber of molelcules
Total (without water)50,3436
Polymers50,3436
Non-polymers00
Water6,539363
1
A: Gem-associated protein 6
B: Gem-associated protein 7

F: Gem-associated protein 8


  • defined by author&software
  • Evidence: gel filtration, The trimeric complex was first purified by a 2-step affinity purification (with different baits each time). Afterwards it was analyzed by gel-filtration and the co-elution ...Evidence: gel filtration, The trimeric complex was first purified by a 2-step affinity purification (with different baits each time). Afterwards it was analyzed by gel-filtration and the co-elution of all 3 proteins was observed, confirmation their interaction.
  • 25.2 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)25,1723
Polymers25,1723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_547-x,y-1/2,-z+5/21
Buried area4060 Å2
ΔGint-30 kcal/mol
Surface area11640 Å2
MethodPISA
2
C: Gem-associated protein 6
D: Gem-associated protein 7
E: Gem-associated protein 8


Theoretical massNumber of molelcules
Total (without water)25,1723
Polymers25,1723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-30 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.880, 80.597, 82.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11E-345-

HOH

21E-346-

HOH

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Components

#1: Protein Gem-associated protein 6 / Gemin-6 / SIP2


Mass: 10537.991 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WXD5
#2: Protein Gem-associated protein 7 / Gemin-7 / SIP3


Mass: 9733.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H840
#3: Protein/peptide Gem-associated protein 8 / Gemin-8 / Protein FAM51A1


Mass: 4900.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN8, FAM51A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NWZ8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM 2-(N-morpholino) ethanesulfonic acid, 200 mM NaCl, 30 % Jeffamine ED2003

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.521→48.494 Å / Num. obs: 58263 / % possible obs: 93.55 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.61 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06668 / Rpim(I) all: 0.03546 / Rrim(I) all: 0.07609 / Net I/σ(I): 10.83
Reflection shellResolution: 1.521→1.576 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.7935 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 4340 / CC1/2: 0.197 / CC star: 0.574 / Rpim(I) all: 0.5227 / Rrim(I) all: 0.9596 / % possible all: 70.86

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Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y96

1y96


Resolution: 1.521→48.494 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 2873 4.95 %
Rwork0.2058 55204 -
obs0.208 58077 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.27 Å2 / Biso mean: 27.442 Å2 / Biso min: 10 Å2
Refinement stepCycle: final / Resolution: 1.521→48.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 0 363 3690
Biso mean---34.46 -
Num. residues----418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5214-1.54630.4366840.4147187467
1.5463-1.5730.40921140.4053204475
1.573-1.60160.42691000.3767224581
1.6016-1.63240.40751200.363243388
1.6324-1.66570.36261450.3468260094
1.6657-1.7020.3661380.3226274998
1.702-1.74160.31121740.2914270999
1.7416-1.78510.30021320.2792278499
1.7851-1.83340.29361490.2615277399
1.8334-1.88730.30241550.2461272398
1.8873-1.94830.30721280.2144271598
1.9483-2.01790.23491490.2083274598
2.0179-2.09870.23691350.1888276898
2.0987-2.19420.26461510.1805272598
2.1942-2.30990.21641380.1814275197
2.3099-2.45460.22741580.1803272897
2.4546-2.64410.25481270.1887275497
2.6441-2.91020.23921490.1925273697
2.9102-3.33120.25141360.1808278097
3.3312-4.19660.18241320.1589279096
4.1966-48.4940.22571590.1821277892

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