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- PDB-2lks: Ff11-60 -

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Basic information

Entry
Database: PDB / ID: 2lks
TitleFf11-60
ComponentsPre-mRNA-processing factor 40 homolog A
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


mRNA cis splicing, via spliceosome / U1 snRNP / U2-type prespliceosome / cytoskeleton organization / mRNA Splicing - Major Pathway / regulation of cytokinesis / nuclear matrix / mRNA splicing, via spliceosome / cell migration / regulation of cell shape ...mRNA cis splicing, via spliceosome / U1 snRNP / U2-type prespliceosome / cytoskeleton organization / mRNA Splicing - Major Pathway / regulation of cytokinesis / nuclear matrix / mRNA splicing, via spliceosome / cell migration / regulation of cell shape / nuclear speck / cell cycle / cell division / RNA binding / nucleoplasm / membrane
Similarity search - Function
FF domain / Pre-mRNA-processing factor Prp40 / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily ...FF domain / Pre-mRNA-processing factor Prp40 / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pre-mRNA-processing factor 40 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsBarette, J. / Velyvis, A. / Religa, T.L. / Korzhnev, D.M. / Kay, L.E.
CitationJournal: J.Phys.Chem.B / Year: 2012
Title: Cross-Validation of the Structure of a Transiently Formed and Low Populated FF Domain Folding Intermediate Determined by Relaxation Dispersion NMR and CS-Rosetta.
Authors: Barette, J. / Velyvis, A. / Religa, T.L. / Korzhnev, D.M. / Kay, L.E.
History
DepositionOct 19, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-processing factor 40 homolog A


Theoretical massNumber of molelcules
Total (without water)5,7761
Polymers5,7761
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)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Pre-mRNA-processing factor 40 homolog A / Fas ligand-associated factor 1 / Formin-binding protein 11 / Formin-binding protein 3 / Huntingtin ...Fas ligand-associated factor 1 / Formin-binding protein 11 / Formin-binding protein 3 / Huntingtin yeast partner A / Huntingtin-interacting protein 10 / HIP-10 / Huntingtin-interacting protein A / Renal carcinoma antigen NY-REN-6


Mass: 5775.674 Da / Num. of mol.: 1 / Fragment: FF 1 domain residues 391-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: FBP11, FLAF1, FNBP3, HIP10, HSPC225, HYPA, Hypa/FBP11, PRPF40A
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75400

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCACONNH
1413D HNCO
1513D HN(CA)CB
1613D HCC-TOCSY
1713D CCC-TOCSY
1813D HACACONNH
1913D NC-NOESY (simultaneous N and C)
11023D methyl-methyl NOESY
11123D 1H(ALA)-13C(ALA)-1H NOESY
11232D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium acetate, 50 mM sodium chloride, 0.05 % sodium azide, 1 mM [U-100% 13C; U-100% 15N] FF11, 95% H2O/5% D2O95% H2O/5% D2O
220 mM sodium acetate, 50 mM sodium chloride, 0.05 % sodium azide, 1 mM [U-100% 13C; U-100% 15N] FF11-60 A51L, 95% H2O/5% D2O95% H2O/5% D2O
320 mM 20mM sodium acetate, 50 mM 50 mM sodium chloride, 0.05 % 0.05% sodium azide, 1 mM [U-10% 13C; U-100% 15N] FF11, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium acetate-11
50 mMsodium chloride-21
0.05 %sodium azide-31
1 mMFF11-60-4[U-100% 13C; U-100% 15N]1
20 mMsodium acetate-52
50 mMsodium chloride-62
0.05 %sodium azide-72
1 mMFF11-60 A51L-8[U-100% 13C; U-100% 15N]2
20 mM20mM sodium acetate-93
50 mM50 mM sodium chloride-103
0.05 %0.05% sodium azide-113
1 mMFF11-60-12[U-10% 13C; U-100% 15N]3
Sample conditionsIonic strength: 0.070 / pH: 4.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5Johnson, One Moon Scientificchemical shift assignment
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorestructure solution
TALOS+Cornilescu, Delaglio and Baxstructure solution
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 122 / NOE intraresidue total count: 0 / NOE long range total count: 27 / NOE medium range total count: 57 / NOE sequential total count: 37 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 29 / Protein psi angle constraints total count: 29
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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