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- PDB-1y96: crystal structure of the Gemin6/Gemin7 heterodimer from the human... -

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Basic information

Entry
Database: PDB / ID: 1y96
Titlecrystal structure of the Gemin6/Gemin7 heterodimer from the human SMN complex
Components
  • Gem-associated protein 6
  • Gem-associated protein 7
KeywordsRNA BINDING PROTEIN / Sm fold / protein complex
Function / homology
Function and homology information


Sm-like protein family complex / Gemini of coiled 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 coiled 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 / cytosol / cytoplasm
Similarity search - Function
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 ...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. / SH3 type barrels. - #100 / : / Sm domain profile. / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Gem-associated protein 6 / Gem-associated protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.002 Å
AuthorsMa, Y. / Dostie, J. / Dreyfuss, G. / Van Duyne, G.D.
CitationJournal: Structure / Year: 2005
Title: The Gemin6-Gemin7 Heterodimer from the Survival of Motor Neurons Complex Has an Sm Protein-like Structure.
Authors: Ma, Y. / Dostie, J. / Dreyfuss, G. / Van Duyne, G.D.
History
DepositionDec 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Gem-associated protein 7
C: Gem-associated protein 6
D: Gem-associated protein 7


Theoretical massNumber of molelcules
Total (without water)38,8684
Polymers38,8684
Non-polymers00
Water1,946108
1
A: Gem-associated protein 6
B: Gem-associated protein 7


Theoretical massNumber of molelcules
Total (without water)19,4342
Polymers19,4342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-20 kcal/mol
Surface area9690 Å2
MethodPISA
2
C: Gem-associated protein 6
D: Gem-associated protein 7


Theoretical massNumber of molelcules
Total (without water)19,4342
Polymers19,4342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-15 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.011, 136.011, 81.515
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Gem-associated protein 6 / / Gemin6 / SIP2


Mass: 9945.347 Da / Num. of mol.: 2 / Fragment: Gemin6(1-86)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN6 / Plasmid: pGV67 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8WXD5
#2: Protein Gem-associated protein 7 / Gemin7 / SIP3


Mass: 9488.716 Da / Num. of mol.: 2 / Fragment: Gemin7(47-131)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN7 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9H840
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.1 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: sodium acetate, MPD, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111.0781
SYNCHROTRONALS 8.2.221.0781
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 24, 2003
ADSC QUANTUM 42CCDJul 24, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.002→50 Å / Num. obs: 49487 / % possible obs: 95.6 % / Observed criterion σ(F): 5
Reflection shellResolution: 2.002→2.054 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.002→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.262 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 5 / ESU R: 0.126 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25177 2516 5.1 %RANDOM
Rwork0.21697 ---
all0.219 46929 --
obs0.21869 49487 95.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.002→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 0 108 2818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212762
X-RAY DIFFRACTIONr_bond_other_d0.0020.022501
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9373733
X-RAY DIFFRACTIONr_angle_other_deg0.7935798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255336
X-RAY DIFFRACTIONr_chiral_restr0.0840.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023056
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02570
X-RAY DIFFRACTIONr_nbd_refined0.1890.2495
X-RAY DIFFRACTIONr_nbd_other0.2420.22727
X-RAY DIFFRACTIONr_nbtor_other0.0850.21693
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.211
X-RAY DIFFRACTIONr_mcbond_it0.8041.51684
X-RAY DIFFRACTIONr_mcangle_it1.60322711
X-RAY DIFFRACTIONr_scbond_it2.49331078
X-RAY DIFFRACTIONr_scangle_it4.3384.51022
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 116
Rwork0.279 2113

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