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- PDB-1b34: CRYSTAL STRUCTURE OF THE D1D2 SUB-COMPLEX FROM THE HUMAN SNRNP CO... -

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Basic information

Entry
Database: PDB / ID: 1b34
TitleCRYSTAL STRUCTURE OF THE D1D2 SUB-COMPLEX FROM THE HUMAN SNRNP CORE DOMAIN
Components
  • PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1)
  • PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2)
KeywordsRNA BINDING PROTEIN / SNRNP / SPLICING / SPLICEOSOME / SM / CORE SNRNP DOMAIN / SYSTEMIC LUPUS ERYTHEMATOSUS / SLE
Function / homology
Function and homology information


U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / U2-type precatalytic spliceosome / commitment complex ...U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / U2-type precatalytic spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / precatalytic spliceosome / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / U5 snRNP / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Small nuclear ribonucleoprotein D1 / SH3 type barrels. - #100 / Small nuclear ribonucleoprotein Sm D2 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily ...Small nuclear ribonucleoprotein D1 / SH3 type barrels. - #100 / Small nuclear ribonucleoprotein Sm D2 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsWalke, S. / Young, R.J. / Kambach, C. / Avis, J.M. / De La Fortelle, E. / Li, J. / Nagai, K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs.
Authors: Kambach, C. / Walke, S. / Young, R. / Avis, J.M. / de la Fortelle, E. / Raker, V.A. / Luhrmann, R. / Li, J. / Nagai, K.
History
DepositionDec 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 1.4Dec 27, 2023Group: 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: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1)
B: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2)


Theoretical massNumber of molelcules
Total (without water)26,8632
Polymers26,8632
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-8 kcal/mol
Surface area8860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.300, 75.300, 91.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1)


Mass: 13310.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#2: Protein PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2)


Mass: 13551.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62316
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium citrate1reservoir
20.2 Mammonium acetate1reservoir
315 %glycerol1reservoir
425 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→18.4 Å / Num. obs: 10307 / % possible obs: 97.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→18.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 994 10 %RANDOM
Rwork0.249 ---
obs-10307 99 %-
Displacement parametersBiso mean: 40.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→18.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 20 1239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.023
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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