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- PDB-1jei: LEM DOMAIN OF HUMAN INNER NUCLEAR MEMBRANE PROTEIN EMERIN -

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Basic information

Entry
Database: PDB / ID: 1jei
TitleLEM DOMAIN OF HUMAN INNER NUCLEAR MEMBRANE PROTEIN EMERIN
ComponentsEMERIN
KeywordsMEMBRANE PROTEIN / emerin nucleus membrane domain dystrophy
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 / nuclear outer membrane / RHOD GTPase cycle / nuclear inner membrane / regulation of canonical Wnt signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane ...TMEM240-body / nuclear membrane organization / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / Initiation of Nuclear Envelope (NE) Reformation / nuclear outer membrane / RHOD GTPase cycle / nuclear inner membrane / regulation of canonical Wnt signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / muscle organ development / beta-tubulin binding / skeletal muscle cell differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of fibroblast proliferation / muscle contraction / RAC1 GTPase cycle / positive regulation of protein export from nucleus / negative regulation of canonical Wnt signaling pathway / cellular response to growth factor stimulus / spindle / nuclear envelope / actin binding / nuclear membrane / microtubule / amyloid fibril formation / 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
MethodSOLUTION NMR / semi-automated iterative procedure using X-PLOR, home-written C-shell programs
AuthorsWolff, N. / Gilquin, B. / Courchay, K. / Callebaut, I. / Zinn-Justin, S.
Citation
Journal: FEBS LETT. / Year: 2001
Title: Structural analysis of emerin, an inner nuclear membrane protein mutated in X-linked Emery-Dreifuss muscular dystrophy
Authors: Wolff, N. / Gilquin, B. / Courchay, K. / Callebaut, I. / Worman, H.J. / Zinn-Justin, S.
#1: Journal: Structure / Year: 2001
Title: Structural characterization of the LEM motif common to three human inner nuclar membrane proteins.
Authors: Laguri, C. / Gilquin, B. / Wolff, N. / Romi-Lebrun, R. / Courchay, K. / Callebaut, I. / Worman, H.J. / Zinn-Justin, S.
History
DepositionJun 18, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 4, 2001Provider: 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 1.4May 29, 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: EMERIN


Theoretical massNumber of molelcules
Total (without water)6,2381
Polymers6,2381
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein EMERIN


Mass: 6237.948 Da / Num. of mol.: 1 / Fragment: LEM DOMAIN (RESIDUES 2-54) / Source method: obtained synthetically / Details: chemical synthesis / References: UniProt: P50402

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: LEM domain of emerin 1mM
Solvent system: NaH2PO4/Na2HPO4 20mM, pH 6.3, 90% H2O/10% D2O or 100% D2O
Sample conditionsIonic strength: 20mM / pH: 6.3 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionClassification
Felix2data analysis
X-PLOR3.1structure solution
X-PLOR3.1refinement
RefinementMethod: semi-automated iterative procedure using X-PLOR, home-written C-shell programs
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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