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- PDB-2fnf: C1 domain of Nore1 -

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Basic information

Entry
Database: PDB / ID: 2fnf
TitleC1 domain of Nore1
Componentsputative Ras Effector Nore1
KeywordsAPOPTOSIS / ZINC / SIGNAL TRANSDUCTION / 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 / identical protein binding / metal ion binding / nucleus / 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-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / 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-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing; molecular dynamics; torsion angle dynamics
AuthorsHarjes, E. / Harjes, S. / Wohlgemuth, S. / Krieger, E. / Herrmann, C. / Muller, K.H. / Bayer, P.
CitationJournal: Structure / Year: 2006
Title: GTP-Ras disrupts the intramolecular complex of C1 and RA domains of Nore1.
Authors: Harjes, E. / Harjes, S. / Wohlgemuth, S. / Muller, K.H. / Krieger, E. / Herrmann, C. / Bayer, P.
History
DepositionJan 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: putative Ras Effector Nore1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4003
Polymers8,2701
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein putative Ras Effector Nore1


Mass: 8269.521 Da / Num. of mol.: 1 / Fragment: cysteine rich domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS / References: GenBank: 2997698, 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 BUFFER90% 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 6.9 ambient 300 K
20.5 mM NAN3 6.9 ambient 300 K
30.5 mM NAN3 6.9 ambient 300 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AURELIA2.8.11Neidigdata analysis
XwinNMR2.5Brukerprocessing
YASARA5.11.29Kriegerstructure solution
YASARA5.11.29Kriegerrefinement
RefinementMethod: simulated annealing; molecular dynamics; torsion angle dynamics
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 583 RESTRAINTS, 501 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 48 DIHEDRAL ANGLE RESTRAINTS, 34 DISTANCE RESTRAINTS FROM HYDROGEN BONDS
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: 30

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