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- PDB-2m4n: Solution structure of the putative Ras interaction domain of AFD-... -

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Basic information

Entry
Database: PDB / ID: 2m4n
TitleSolution structure of the putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans
ComponentsProtein AFD-1, isoform a
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / THIOREDOXIN-LIKE / New York Structural Genomics Research Consortium / NYSGRC / Assembly / Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions / CELLMAT / PSI-Biology
Function / homology
Function and homology information


cell adhesion molecule binding / adherens junction / regulation of protein localization / cell adhesion / signal transduction
Similarity search - Function
: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras-associating (RA) domain ...: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulating annealing
Model detailslowest energy, model 1
AuthorsHarris, R. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Chamala, S. / Evans, B. / Lafleur, J. / Hammonds, J. / Washington, E. / Stead, M. ...Harris, R. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Chamala, S. / Evans, B. / Lafleur, J. / Hammonds, J. / Washington, E. / Stead, M. / Love, J. / Attonito, J. / Seidel, R.D. / Liddington, R.C. / Weis, W.I. / Nelson, W.J. / Girvin, M.E. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions (CELLMAT)
CitationJournal: To be Published
Title: Solution structure of the putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans
Authors: Harris, R. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Chamala, S. / Evans, B. / Lafleur, J. / Hammonds, J. / Washington, E. / Stead, M. / Love, J. / Attonito, J. / Seidel, R.D. / Chook, Y. ...Authors: Harris, R. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Chamala, S. / Evans, B. / Lafleur, J. / Hammonds, J. / Washington, E. / Stead, M. / Love, J. / Attonito, J. / Seidel, R.D. / Chook, Y.M. / Rout, M.P. / Liddington, R.C. / Weis, W.I. / Nelson, W.J. / Girvin, M.E. / Almo, S.C.
History
DepositionFeb 7, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 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: Protein AFD-1, isoform a


Theoretical massNumber of molelcules
Total (without water)11,9721
Polymers11,9721
Non-polymers00
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 / 10020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein AFD-1, isoform a


Mass: 11972.441 Da / Num. of mol.: 1 / Fragment: UNP residues 214-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: afd-1, W03F11.6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BIC1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HSQC
12115N NOESY-HSQC
13213C HSQC
142aromatic 13C HSQC
15213C NOESY-HSQC
16213C aromatic NOESY-HSQC
171HNCO
181HN(CA)CO
191HNCA
1101HN(CO)CA
1111HN(CA)CB
1121CBCA(CO)NH
NMR detailsText: All 3D experiments were acquired using 30% non-uniform sampling using the MDDNMR approach

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] putative Ras interaction domain of AFD, isoform a, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.1 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] putative Ras interaction domain of AFD, isoform a, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMputative Ras interaction domain of AFD-1, isoform a-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMDTT-41
0.1 mMEDTA-51
1.0 mMputative Ras interaction domain of AFD-1, isoform a-6[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-72
50 mMsodium chloride-82
1 mMDTT-92
0.1 mMEDTA-102
Sample conditionsIonic strength: 70 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger A. T. et.al.refinement
VnmrJ2.2DVariancollection
TopSpin1.3 & 2.1Bruker Biospincollection
NMRPipe7.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MddNMR2.2(MDDNMR) Orekhov, Jaravine, Kazimierczukcollection
MddNMR2.2(MDDNMR) Orekhov, Jaravine, Kazimierczukprocessing
MDDGUI1(MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmithcollection
MDDGUI1(MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmithprocessing
CCPN_AnalysisCCPNdata analysis
ARIA2.3Linge, O'Donoghue and Nilgesdata analysis
SideRHansendata analysis
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulating annealing / Software ordinal: 1 / Details: Refinement in a box of water
NMR constraintsNOE constraints total: 1754 / NOE intraresidue total count: 513 / NOE long range total count: 577 / NOE medium range total count: 215 / NOE sequential total count: 361 / Protein other angle constraints total count: 27 / Protein phi angle constraints total count: 46 / Protein psi angle constraints total count: 46
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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