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- PDB-5xjl: Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in ... -

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Basic information

Entry
Database: PDB / ID: 5xjl
TitleCrystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with SmD1/D2/F/E/G from Human
Components
  • (Small nuclear ribonucleoprotein ...) x 5
  • Gem-associated protein 2
  • Survival motor neuron protein
KeywordsSPLICING
Function / homology
Function and homology information


: / Gemini of Cajal bodies / SMN complex / U7 snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / U1 snRNP binding / methylosome ...: / Gemini of Cajal bodies / SMN complex / U7 snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / U1 snRNP binding / methylosome / RNA splicing, via transesterification reactions / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type precatalytic spliceosome / commitment complex / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / RNA Polymerase II Transcription Termination / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / spliceosomal snRNP assembly / Cajal body / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / DNA-templated transcription termination / mRNA splicing, via spliceosome / Z disc / cytoplasmic ribonucleoprotein granule / mRNA processing / nervous system development / snRNP Assembly / perikaryon / SARS-CoV-2 modulates host translation machinery / neuron projection / nuclear body / axon / nucleolus / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Gem-associated protein 2 / Gemin2/Brr1 / Survival motor neuron (SMN) interacting protein 1 (SIP1) / : / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : / Survival motor neuron, Tudor domain ...Gem-associated protein 2 / Gemin2/Brr1 / Survival motor neuron (SMN) interacting protein 1 (SIP1) / : / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Small nuclear ribonucleoprotein D1 / SH3 type barrels. - #100 / Tudor domain / Small nuclear ribonucleoprotein Sm D2 / Tudor domain / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / 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
Gem-associated protein 2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Survival motor neuron protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, R.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570720 China
National Natural Science Foundation of China81441109 China
CitationJournal: Cell / Year: 2011
Title: Structure of a key intermediate of the SMN complex reveals Gemin2's crucial function in snRNP assembly
Authors: Zhang, R. / So, B.R. / Li, P. / Yong, J. / Glisovic, T. / Wan, L. / Dreyfuss, G.
History
DepositionMay 2, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 2, 2018ID: 3S6N
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
2: Gem-associated protein 2
A: Small nuclear ribonucleoprotein Sm D1
B: Small nuclear ribonucleoprotein Sm D2
E: Small nuclear ribonucleoprotein E
F: Small nuclear ribonucleoprotein F
G: Small nuclear ribonucleoprotein G
M: Survival motor neuron protein


Theoretical massNumber of molelcules
Total (without water)91,5907
Polymers91,5907
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15050 Å2
ΔGint-84 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.830, 84.600, 104.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Small nuclear ribonucleoprotein ... , 5 types, 5 molecules ABEFG

#2: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62314
#3: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD2, SNRPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62316
#4: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPE / Production host: Escherichia coli (E. coli) / References: UniProt: P62304
#5: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPF, PBSCF / Production host: Escherichia coli (E. coli) / References: UniProt: P62306
#6: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPG, PBSCG / Production host: Escherichia coli (E. coli) / References: UniProt: P62308

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Protein / Protein/peptide / Non-polymers , 3 types, 33 molecules 2M

#1: Protein Gem-associated protein 2 / Gemin-2 / Component of gems 2 / Survival of motor neuron protein-interacting protein 1 / SMN- ...Gemin-2 / Component of gems 2 / Survival of motor neuron protein-interacting protein 1 / SMN-interacting protein 1


Mass: 31620.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN2, SIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14893
#7: Protein/peptide Survival motor neuron protein / Component of gems 1 / Gemin-1


Mass: 4047.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMN1, SMN, SMNT, SMN2, SMNC / Production host: Escherichia coli (E. coli) / References: UniProt: Q16637
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1%PEG8000, 100mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99993 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 2.5→59.19 Å / Num. obs: 19831 / % possible obs: 99.3 % / Redundancy: 6.3 % / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→59.19 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.854 / SU B: 0.006 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2957 1015 5.1 %RANDOM
Rwork0.2198 ---
obs0.2238 18815 76.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.65 Å2 / Biso mean: 52.21 Å2 / Biso min: 8.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 2.5→59.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4795 0 0 31 4826
Biso mean---31.51 -
Num. residues----601
LS refinement shellResolution: 2.502→2.566 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 16 -
Rwork0.392 271 -
all-287 -
obs--15.15 %

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