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- PDB-2leh: Solution structure of the core SMN-Gemin2 complex -

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Basic information

Entry
Database: PDB / ID: 2leh
TitleSolution structure of the core SMN-Gemin2 complex
Components
  • Survival motor neuron proteinSurvival of motor neuron
  • Survival of motor neuron protein-interacting protein 1
KeywordsPROTEIN BINDING / Spinal Muscular Atrophy / snRNP assembly
Function / homology
Function and homology information


negative regulation of RNA binding / Gemini of coiled bodies / SMN complex / RNA splicing, via transesterification reactions / SMN-Sm protein complex / spliceosomal complex assembly / Cajal body / spliceosomal snRNP assembly / RNA splicing / DNA-templated transcription termination ...negative regulation of RNA binding / Gemini of coiled bodies / SMN complex / RNA splicing, via transesterification reactions / SMN-Sm protein complex / spliceosomal complex assembly / Cajal body / spliceosomal snRNP assembly / RNA splicing / DNA-templated transcription termination / spliceosomal complex / cytoplasmic ribonucleoprotein granule / mRNA processing / Z disc / snRNP Assembly / nervous system development / SARS-CoV-2 modulates host translation machinery / perikaryon / nuclear body / neuron projection / axon / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1070 / Gem-associated protein 2 / Gemin2/Brr1 / Survival motor neuron (SMN) interacting protein 1 (SIP1) / SMN complex subunit Smn1 / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / : / Survival motor neuron, Tudor domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1070 / Gem-associated protein 2 / Gemin2/Brr1 / Survival motor neuron (SMN) interacting protein 1 (SIP1) / SMN complex subunit Smn1 / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Gem-associated protein 2 / Survival motor neuron protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSarachan, K.L. / Valentine, K. / Gupta, K. / Moorman, V. / Gledhill, J. / Bernens, M. / Tommos, C. / Wand, A.J. / Van Duyne, G.
CitationJournal: Biochem.J. / Year: 2012
Title: Solution structure of the core SMN-Gemin2 complex.
Authors: Sarachan, K.L. / Valentine, K.G. / Gupta, K. / Moorman, V.R. / Gledhill Jr, J.M. / Bernens, M. / Tommos, C. / Wand, A.J. / Van Duyne, G.D.
History
DepositionJun 15, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: database_2 / pdbx_nmr_exptl ...database_2 / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name / _pdbx_nmr_software.version / _pdbx_nmr_spectrometer.model / _struct.pdbx_model_details / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Survival of motor neuron protein-interacting protein 1
B: Survival motor neuron protein


Theoretical massNumber of molelcules
Total (without water)24,4732
Polymers24,4732
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 21609.434 Da / Num. of mol.: 1 / Fragment: UNP residues 95-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIP1, GEMIN2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14893
#2: Protein/peptide Survival motor neuron protein / Survival of motor neuron / Component of gems 1 / Gemin-1


Mass: 2863.072 Da / Num. of mol.: 1 / Fragment: UNP residues 26-51
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) / Strain (production host): BL21(DE3) / References: UniProt: Q16637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HN(CA)CO
1713D HNCO
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11222D 1H-13C HSQC aromatic
11323D 1H-13C NOESY aromatic
11413D (H)CCH-TOCSY aromatic
11542D 1H-15N HSQC
11652D 1H-15N HSQC
11732D 1H-13C HSQC
11814D HNCH-NOESY-HSQC
11924D (H)CCH-NOESY-HMQC
12062D 1H-15N HSQC IPAP
12172D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-99% 13C; U-99% 15N] gemin2, 1.0 mM [U-99% 13C; U-99% 15N] smn, 50 mM sodium chloride, 50 mM DTT, 50 uM EDTA, 200 nM sodium azide, 34.25 mM sodium phosphate, 15.75 mM potassium phosphate, 95% H2O/5% D2Osample_195% H2O/5% D2O
solution21.0 mM [U-99% 13C; U-99% 15N] gemin2, 1.0 mM [U-99% 13C; U-99% 15N] smn, 50 mM sodium chloride, 50 mM [U-98% 2H] DTT, 50 uM EDTA, 200 nM sodium azide, 34.25 mM sodium phosphate, 15.75 mM potassium phosphate, 100% D2Osample_2100% D2O
solution31.0 mM [U-10% 13C; U-99% 15N] gemin2, 1.0 mM [U-10% 13C; U-99% 15N] smn, 50 mM sodium chloride, 50 mM DTT, 50 uM EDTA, 200 nM sodium azide, 34.25 mM sodium phosphate, 15.75 mM potassium phosphate, 95% H2O/5% D2Osample_395% H2O/5% D2O
solution41.0 mM [U-98% 15N]-Leu gemin2, 1.0 mM smn, 50 mM sodium chloride, 50 mM DTT, 50 uM EDTA, 200 nM sodium azide, 34.25 mM sodium phosphate, 15.75 mM potassium phosphate, 95% H2O/5% D2Osample_495% H2O/5% D2O
solution51.0 mM gemin2, 1.0 mM [U-99% 15N] smn, 50 mM sodium chloride, 50 mM DTT, 50 uM EDTA, 200 nM sodium azide, 34.25 mM sodium phosphate, 15.75 mM potassium phosphate, 95% H2O/5% D2Osample_595% H2O/5% D2O
bicelle61.0 mM [U-99% 15N] gemin2, 1.0 mM [U-99% 15N] smn, 50 mM sodium chloride, 50 mM DTT, 50 uM EDTA, 200 nM sodium azide, 34.25 mM sodium phosphate, 15.75 mM potassium phosphate, 12 mg/ml bacteriophage Pf1 strain LP11-92, 90% H2O/10% D2Osample_690% H2O/10% D2O
solution71.0 mM [U-99% 15N] gemin2 C154S/C221S/C264S mutant labeled with S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate (MTSL) at C241, 1.0 mM [U-99% 15N] smn, 50 mM sodium chloride, 50 mM DTT, 50 uM EDTA, 200 nM sodium azide, 34.25 mM sodium phosphate, 15.75 mM potassium phosphate, 95% H2O/5% D2Osample_790% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMgemin2[U-99% 13C; U-99% 15N]1
1.0 mMsmn[U-99% 13C; U-99% 15N]1
50 mMsodium chloridenatural abundance1
50 mMDTTnatural abundance1
50 uMEDTAnatural abundance1
200 uMsodium azidenatural abundance1
34.25 mMsodium phosphatenatural abundance1
15.75 mMpotassium phosphatenatural abundance1
1.0 mMgemin2[U-99% 13C; U-99% 15N]2
1.0 mMsmn[U-99% 13C; U-99% 15N]2
50 mMsodium chloridenatural abundance2
50 mMDTT[U-98% 2H]2
50 uMEDTAnatural abundance2
200 uMsodium azidenatural abundance2
34.25 mMsodium phosphatenatural abundance2
15.75 mMpotassium phosphatenatural abundance2
1.0 mMgemin2[U-10% 13C; U-99% 15N]3
1.0 mMsmn[U-10% 13C; U-99% 15N]3
50 mMsodium chloridenatural abundance3
50 mMDTTnatural abundance3
50 uMEDTAnatural abundance3
200 uMsodium azidenatural abundance3
34.25 mMsodium phosphatenatural abundance3
15.75 mMpotassium phosphatenatural abundance3
1.0 mMgemin2[U-98% 15N]-Leu4
1.0 mMsmnnatural abundance4
50 mMsodium chloridenatural abundance4
50 mMDTTnatural abundance4
50 uMEDTAnatural abundance4
200 uMsodium azidenatural abundance4
34.25 mMsodium phosphatenatural abundance4
15.75 mMpotassium phosphatenatural abundance4
1.0 mMgemin2natural abundance5
1.0 mMsmn[U-99% 15N]5
50 mMsodium chloridenatural abundance5
50 mMDTTnatural abundance5
50 uMEDTAnatural abundance5
200 uMsodium azidenatural abundance5
34.25 mMsodium phosphatenatural abundance5
15.75 mMpotassium phosphatenatural abundance5
1.0 mMgemin2[U-99% 15N]6
1.0 mMsmn[U-99% 15N]6
50 mMsodium chloridenatural abundance6
50 mMDTTnatural abundance6
50 uMEDTAnatural abundance6
200 uMsodium azidenatural abundance6
34.25 mMsodium phosphatenatural abundance6
15.75 mMpotassium phosphatenatural abundance6
12 mg/mLbacteriophage Pf1 strain LP11-92natural abundance6
1.0 mMgemin2 C154S/C221S/C264S mutant labeled with S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate (MTSL) at C241[U-99% 15N]7
1.0 mMsmn[U-99% 15N]7
50 mMsodium chloridenatural abundance7
50 mMDTTnatural abundance7
50 uMEDTAnatural abundance7
200 nMsodium azidenatural abundance7
34.25 mMsodium phosphatenatural abundance7
15.75 mMpotassium phosphatenatural abundance7
Sample conditionsIonic strength: not calculated / pH: 6.5 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7501
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorestructure solution
FelixAccelrys Software Inc.processing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
Details: RESIDUAL DIPOLAR COUPLINGS (RDCS), LONG-DISTANCE RESTRAINTS FROM PARAMAGNETIC RELAXATION ENHANCEMENTS (PRES) AND SMALL-ANGLE X-RAY SCATTERING WERE EMPLOYED AS RESTRAINTS.
NMR constraintsNOE constraints total: 1849 / NOE intraresidue total count: 616 / NOE long range total count: 239 / NOE medium range total count: 453 / NOE sequential total count: 541 / Hydrogen bond constraints total count: 55 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 139 / Protein psi angle constraints total count: 134
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 32

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