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- PDB-1fho: Solution Structure of the PH Domain from the C. Elegans Muscle Pr... -

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Basic information

Entry
Database: PDB / ID: 1fho
TitleSolution Structure of the PH Domain from the C. Elegans Muscle Protein UNC-89
ComponentsUNC-89
KeywordsSIGNALING PROTEIN / Pleckstrin Homology domain / electrostatics / muscle / signal transduction
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity => GO:0005085 / small GTPase binding => GO:0031267 / nematode pharyngeal gland morphogenesis / Cross-presentation of soluble exogenous antigens (endosomes) / : / Platelet sensitization by LDL / regulation of skeletal muscle contraction by calcium ion signaling / protein localization => GO:0008104 / Integrin cell surface interactions / Platelet degranulation ...guanyl-nucleotide exchange factor activity => GO:0005085 / small GTPase binding => GO:0031267 / nematode pharyngeal gland morphogenesis / Cross-presentation of soluble exogenous antigens (endosomes) / : / Platelet sensitization by LDL / regulation of skeletal muscle contraction by calcium ion signaling / protein localization => GO:0008104 / Integrin cell surface interactions / Platelet degranulation / positive regulation of locomotion / MATH domain binding / striated muscle myosin thick filament assembly / Neutrophil degranulation / plasma membrane => GO:0005886 / positive regulation of sarcomere organization / myosin filament assembly / positive regulation of striated muscle contraction / positive regulation of protein localization to endoplasmic reticulum / skeletal muscle myosin thick filament assembly / M band / A band / sarcomere organization / phosphatase binding / protein kinase activity / positive regulation of gene expression / ATP binding
Similarity search - Function
RCSD / RCSD region / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Immunoglobulin I-set ...RCSD / RCSD region / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain profile. / Pleckstrin homology domain. / Fibronectin type III domain / Pleckstrin homology domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Muscle M-line assembly protein unc-89
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / Automated NOE assignment,Torsion angle dynamics, Cartesian simulated annealing.
AuthorsBlomberg, N. / Baraldi, E. / Sattler, M. / Saraste, M. / Nilges, M.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Structure of a PH domain from the C. elegans muscle protein UNC-89 suggests a novel function.
Authors: Blomberg, N. / Baraldi, E. / Sattler, M. / Saraste, M. / Nilges, M.
#1: Journal: J.Biomol.NMR / Year: 1999
Title: 1H, 15N, and 13C Resonance Assignment of the PH Domain from C. elegans UNC-89
Authors: Blomberg, N. / Sattler, M. / Nilges, M.
#2: Journal: Proteins / Year: 1999
Title: Classification of Protein Sequences by Homology Modelling and Quantitative Analysis of Electrostatic Similarity
Authors: Blomberg, N. / Gabdoulline, R.R. / Nilges, M. / Wade, R.C.
#3: Journal: Fold.Des. / Year: 1997
Title: Functional Diversity of PH Domains: an Exhaustive Modelling Study
Authors: Blomberg, N. / Nilges, M.
History
DepositionAug 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UNC-89


Theoretical massNumber of molelcules
Total (without water)14,1041
Polymers14,1041
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)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein UNC-89


Mass: 14103.741 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY (PH) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: PBAT4 / Production host: Escherichia coli (E. coli) / References: UniProt: O01761

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
34315N HSQC not decoupled
NMR detailsText: Structure determined using triple resonance NMR techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
1800 uM UNC-89 PH domain 13C,15N; 5mM sodium phosphate95% H2O/ 5% D2O; 15% dDMSO added to sample
2800 uM UNC-89 PH domain 15N; 5mM sodium phosphate95% H2O/ 5% D2O; 15% dDMSO added to sample
3800 uM UNC-89 PH domain 15N; 5mM sodium phosphate95% H2O/ 5% D2O; DMPC/DLPC/SDS (ratio 3.2:1:0.1; 5% w/v total lipid)
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15mM 6.8ambient 303 K
25mM 6.8ambient 303 K
35mM 6.8ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Brukercollection
NMRPipe1.7Delaglio et alprocessing
XEASY1.3.13Xia et aldata analysis
ARIA0.5Nilgesstructure solution
CNS0.5Brunger et alstructure solution
CNS0.5Brunger et alrefinement
RefinementMethod: Automated NOE assignment,Torsion angle dynamics, Cartesian simulated annealing.
Software ordinal: 1
Details: The structure was calculated automated NOE assignment and structure calculation using ARIA/CNS. Manual NOE assignments were added between cycles of automated assignment. The final structures ...Details: The structure was calculated automated NOE assignment and structure calculation using ARIA/CNS. Manual NOE assignments were added between cycles of automated assignment. The final structures were refined in a shell of explicit solvent. Data consisted of: 1230 unique NOE restaints; 44 phi restraints (3JHNHA scalar couplings, direct refinement against couplings); 41 1JHN residual dipolar couplings. Final ensemble was refined in explicit water.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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