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- PDB-2n62: ddFLN5+110 -

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Basic information

Entry
Database: PDB / ID: 2n62
TitleddFLN5+110
Componentsgelation factor, secretion monitor chimera
KeywordsTRANSLATION
Function / homology
Function and homology information


regulation of pseudopodium assembly / anterior cell cortex / pseudopodium assembly / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / protein kinase B binding ...regulation of pseudopodium assembly / anterior cell cortex / pseudopodium assembly / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / protein kinase B binding / actin crosslink formation / thermotaxis / hyperosmotic response / mitogen-activated protein kinase binding / lamellipodium assembly / phagocytic cup / cortical actin cytoskeleton / cell leading edge / pseudopodium / translation regulator activity / phagocytosis / response to cAMP / extracellular matrix / cell motility / small GTPase binding / cell migration / actin filament binding / regulation of translation / cell cortex / actin cytoskeleton organization / periplasmic space / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Secretion monitor / Secretion monitor precursor protein (SecM) / Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. ...Secretion monitor / Secretion monitor precursor protein (SecM) / Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Gelation factor / Secretion monitor
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
Escherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsCabrita, L.D. / Cassaignau, A.M.E. / Launay, H.M.M. / Waudby, C.A. / Camilloni, C. / Robertson, A.L. / Wang, X. / Wlodarski, T. / Wentink, A.S. / Vendruscolo, M. ...Cabrita, L.D. / Cassaignau, A.M.E. / Launay, H.M.M. / Waudby, C.A. / Camilloni, C. / Robertson, A.L. / Wang, X. / Wlodarski, T. / Wentink, A.S. / Vendruscolo, M. / Dobson, C.M. / Christodoulou, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: A structural ensemble of a ribosome-nascent chain complex during cotranslational protein folding.
Authors: Cabrita, L.D. / Cassaignau, A.M. / Launay, H.M. / Waudby, C.A. / Wlodarski, T. / Camilloni, C. / Karyadi, M.E. / Robertson, A.L. / Wang, X. / Wentink, A.S. / Goodsell, L.S. / Woolhead, C.A. ...Authors: Cabrita, L.D. / Cassaignau, A.M. / Launay, H.M. / Waudby, C.A. / Wlodarski, T. / Camilloni, C. / Karyadi, M.E. / Robertson, A.L. / Wang, X. / Wentink, A.S. / Goodsell, L.S. / Woolhead, C.A. / Vendruscolo, M. / Dobson, C.M. / Christodoulou, J.
History
DepositionAug 10, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: gelation factor, secretion monitor chimera


Theoretical massNumber of molelcules
Total (without water)23,4211
Polymers23,4211
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)3 / 1500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein gelation factor, secretion monitor chimera / ddFLN5+110


Mass: 23420.723 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum, Escherichia coli
Production host: Escherichia coli (E. coli) / References: UniProt: P13466, UniProt: P62395
Sequence detailsPROTEIN IS A CHIMERA COMPRISING RESIDUES 646-839 OF P13466 LINKED TO RESIDUES 150-166 OF P62395.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structural ensemble of ddFLN5+110 RNC: 3 representative ground state structures
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N SOFAST HMQC
1222D 1H-13C HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
110 uM [U-15N] ddFLN5+110, 10 mM HEPES, 30 mM ammonium chloride, 12 mM MgCl2, 2 mM BME, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
210 uM [U-100% 2H, Ile d1-13CH3] ddFLN5+110, 10 mM [U-2H] HEPES, 30 mM [U-2H] ammonium chloride, 12 mM [U-2H] MgCl2, 2 mM [U-2H] BME, 1 mM [U-2H] EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 uMddFLN5+110-1[U-15N]1
10 mMHEPES-21
30 mMammonium chloride-31
12 mMMgCl2-41
2 mMBME-51
1 mMEDTA-61
10 uMddFLN5+110-7[U-100% 2H, Ile d1-13CH3]2
10 mMHEPES-8[U-2H]2
30 mMammonium chloride-9[U-2H]2
12 mMMgCl2-10[U-2H]2
2 mMBME-11[U-2H]2
1 mMEDTA-12[U-2H]2
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
GROMACS5.0.4GROMACSstructure calculation using molecular dynamics simulations with chemical shifts restraints
GROMACSrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1500 / Conformers submitted total number: 3

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