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- PDB-4a4g: Solution structure of SMN Tudor domain in complex with asymmetric... -

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Basic information

Entry
Database: PDB / ID: 4a4g
TitleSolution structure of SMN Tudor domain in complex with asymmetrically dimethylated arginine
ComponentsSURVIVAL MOTOR NEURON PROTEIN
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development ...Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / perikaryon / nuclear body / neuron projection / axon / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / 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. / Tudor domain ...: / : / 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. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
NG,NG-DIMETHYL-L-ARGININE / Survival motor neuron protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTripsianes, K. / Madl, T. / Machyna, M. / Fessas, D. / Englbrecht, C. / Fischer, U. / Neugebauer, K.M. / Sattler, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural Basis for Dimethyl-Arginine Recognition by the Tudor Domains of Human Smn and Spf30 Proteins
Authors: Tripsianes, K. / Madl, T. / Machyna, M. / Fessas, D. / Englbrecht, C. / Fischer, U. / Neugebauer, K.M. / Sattler, M.
History
DepositionOct 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Dec 28, 2011Group: Other
Revision 1.3Nov 6, 2013Group: Atomic model / Derived calculations
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SURVIVAL MOTOR NEURON PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2962
Polymers7,0941
Non-polymers2021
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein SURVIVAL MOTOR NEURON PROTEIN / SURVIVAL MOTOR NEURON PROTEIN SMN / COMPONENT OF GEMS 1 / GEMIN-1


Mass: 7093.893 Da / Num. of mol.: 1 / Fragment: TUDOR DOMAIN, RESIDUES 84-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q16637
#2: Chemical ChemComp-DA2 / NG,NG-DIMETHYL-L-ARGININE / ADMA


Type: L-peptide linking / Mass: 202.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N4O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-EDITED 3D NOESY
221F1 15N/13C FILTERED
23115N- EDITED 3D NOESY
34113C- EDITED 3D NOESY (ALIPHATICS)
451F1 15N/13C FILTERED
46113C-EDITED 3D NOESY (ALIPHATICS)
57113C- EDITED 3D NOESY (AROMATICS)
681F1 15N/13C FILTERED
69113C-EDITED 3D NOESY (AROMATICS)
NMR detailsText: NONE

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Sample preparation

DetailsContents: 93% WATER/7% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM6.51.0 atm298.0 K
250 mM6.51.0 atm298.0 K
350 mM6.51.0 atm298.0 K
450 mM6.51.0 atm298.0 K
550 mM6.51.0 atm298.0 K
650 mM6.51.0 atm298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
TALOSstructure solution
CYANAstructure solution
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE SET OF NOE DISTANCE RESTRAINTS DERIVED FROM CYANA, PHI AND PSI BACKBONE DIHEDRAL ANGLE RESTRAINTS DERIVED FROM TALOS BASED ON THE CHEMICAL SHIFTS, AND HYDROGEN BONDS WERE USED FOR WATER REFINEMENT USING CNS
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 20

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