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- PDB-2odc: LEM-domain of the nuclear envelope protein emerin -

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Basic information

Entry
Database: PDB / ID: 2odc
TitleLEM-domain of the nuclear envelope protein emerin
ComponentsEmerin
KeywordsMEMBRANE PROTEIN / INNER NUCLEAR MEMBRANE PROTEIN / LEM-DOMAIN MULTIDIMENSIONAL NMR DIPOLAR COUPLINGS
Function / homology
Function and homology information


TMEM240-body / nuclear membrane organization / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / nuclear outer membrane / regulation of canonical Wnt signaling pathway / muscle organ development / nuclear inner membrane ...TMEM240-body / nuclear membrane organization / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / nuclear outer membrane / regulation of canonical Wnt signaling pathway / muscle organ development / nuclear inner membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / beta-tubulin binding / skeletal muscle cell differentiation / RHOG GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / negative regulation of fibroblast proliferation / RAC1 GTPase cycle / positive regulation of protein export from nucleus / muscle contraction / negative regulation of canonical Wnt signaling pathway / spindle / cellular response to growth factor stimulus / nuclear envelope / actin binding / nuclear membrane / microtubule / cadherin binding / endoplasmic reticulum / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Emerin, LEM domain / Emerin / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #40 / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins / LEM/LEM-like domain superfamily / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / RESTRAINED SIMULATED ANNEALING IN TORION ANGLE SPACE
Model type detailsminimized average
AuthorsClore, G.M. / Cai, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Solution NMR Structure of the Barrier-to-Autointegration Factor-Emerin Complex.
Authors: Cai, M. / Huang, Y. / Suh, J.Y. / Louis, J.M. / Ghirlando, R. / Craigie, R. / Clore, G.M.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 7 IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL ... IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. STRUCTURAL STATISTICS: --------------------------------------------------------- DEVIATIONS FROM IDEALIZED GEOMETRY: BONDS 0.004 A ANGLES 0.39 DEG IMPROPERS 0.58 DEG RMS DEVIATIONS FROM EXPT RESTRAINTS NOES (489) 0.016 A TORSION ANGLES (129) 0.32 DEG 13C CA CHEMICAL SHIFTS (47) 1.27 PPM 13C CB CHEMICAL SHIFTS (45) 0.70 PPM DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012): 1DNH (38) 2.3% 1DNC' (36) 11.5% 2DHNC' (36) 12.8% % RESIDUES IN MOST FAVORABLE REGION OF RAMACHADRAN MAP 99.5% -------------------------------------------------------- COORDINATE PRECISION (RESIDUES 2-46): BACKBONE: 0.20(+/-0.06) A ALL HEAVY ATOMS: 0.87(+/-0.09) A

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Emerin


Theoretical massNumber of molelcules
Total (without water)5,7201
Polymers5,7201
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)1 / 180RESTRAINED REGULARIZED MEAN STRUCTURE
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Emerin /


Mass: 5720.397 Da / Num. of mol.: 1 / Fragment: residues 2-47
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUSCell nucleus / Gene: EMD, EDMD, STA / Production host: Escherichia coli (E. coli) / References: UniProt: P50402

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DOUBLE AND TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN
121QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
1313D SEPARATED NOE EXPERIMENTS
1412D HETERONUCLEAR FOR DIPOLAR COUPLING MEASUREMENTS IN LIQUID CRYSTALLINE MEDIUM OF PHAGE PF1

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Sample preparation

Sample conditionsIonic strength: 50 mM POTASSIUM PHOSPHATE / pH: 6.50 / Temperature: 303.00 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX7503
Bruker DRXBrukerDRX8004

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSCHWIETERS, KUSZEWSKI, CLORErefinement
XPLOR-NIHstructure solution
RefinementMethod: RESTRAINED SIMULATED ANNEALING IN TORION ANGLE SPACE
Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE. THE TARGET FUNCTION COMPRISES TERMS FOR THE THE NOE RESTRAINTS, TORSION ANGLE RESTRAINTS, CARBON CHEMICAL SHIFT ...Details: THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE. THE TARGET FUNCTION COMPRISES TERMS FOR THE THE NOE RESTRAINTS, TORSION ANGLE RESTRAINTS, CARBON CHEMICAL SHIFT RESTRAINTS, THE DIPOLAR COUPLING RESTRAINTS, THE RADIUS OF GYRATION, A QUARTIC VAN DER WAALS REPULSION TERM, A MULTIDIMENSIONAL TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE, AND A MULTIDIMENSIONAL HYDROGEN BONDING
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: RESTRAINED REGULARIZED MEAN STRUCTURE
Conformers calculated total number: 180 / Conformers submitted total number: 1

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