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- PDB-1rfh: Solution structure of the C1 domain of Nore1, a novel Ras effector -

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Basic information

Entry
Database: PDB / ID: 1rfh
TitleSolution structure of the C1 domain of Nore1, a novel Ras effector
ComponentsRas association (RalGDS/AF-6) domain family 5
KeywordsMETAL BINDING PROTEIN / ZINC / SIGNAL TRANSDUCTION / APOPTOSIS / CYSTEINE RICH DOMAIN
Function / homology
Function and homology information


negative regulation of lymphocyte proliferation / lymphocyte proliferation / regulation of protein localization to nucleus / positive regulation of protein ubiquitination / microtubule / apoptotic process / signal transduction / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Ras association domain-containing protein 5 / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / SARAH domain / SARAH domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain ...Ras association domain-containing protein 5 / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / SARAH domain / SARAH domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ras association domain-containing protein 5 / Ras association domain-containing protein 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
Model type detailsminimized average
AuthorsGuiberman, E. / Wohlgemuth, S. / Herrmann, C. / Harjes, S. / Mueller, K.H. / Bayer, P.
CitationJournal: To be Published
Title: The solution structure of C1 domain of Nore1
Authors: Guiberman, E. / Wohlgemuth, S. / Herrmann, C. / Harjes, S. / Mueller, K.H. / Bayer, P.
History
DepositionNov 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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: Ras association (RalGDS/AF-6) domain family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8303
Polymers6,6991
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Ras association (RalGDS/AF-6) domain family 5 / novel ras effector 1 / Rap1-binding protein


Mass: 6698.818 Da / Num. of mol.: 1 / Fragment: cysteine-rich domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RASSF5 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus / References: UniProt: O70407, UniProt: Q5EBH1*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
2423D 15N-separated NOESY
3533D 13C-separated NOESY
363HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.6MM C1 DOMAIN UNLABELED, 20mM phosphate buffer K90% H2O/10% D2O
22MM C1 DOMAIN U-15N, 20mM phosphate buffer K90% H2O/10% D2O
32MM C1 DOMAIN U-15N/13C, 20mM phosphate buffer K90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.5 mM NaN3 6.9ambient 300 K
20.5 mM NaN3 6.9ambient 300 K
30.5 mM NaN3 6.9ambient 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AURELIA2.8.11brukerdata analysis
XwinNMR2.5brukerprocessing
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 557 restraints, 475 are NOE-derived distance constraints, 48 dihedral angle restraints, 34 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 21

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