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- PDB-1gjj: N-TERMINAL CONSTANT REGION OF THE NUCLEAR ENVELOPE PROTEIN LAP2 -

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Basic information

Entry
Database: PDB / ID: 1gjj
TitleN-TERMINAL CONSTANT REGION OF THE NUCLEAR ENVELOPE PROTEIN LAP2
ComponentsLAP2
KeywordsMEMBRANE PROTEIN / INNER NUCLEAR MEMBRANE PROTEIN / LAMIN-ASSOCIATED POLYPEPTIDE / LEM DOMAIN / MULTIDIMENSIONAL NMR DIPOLAR COUPLINGS
Function / homology
Function and homology information


lamin binding / nuclear envelope / cadherin binding / chromatin / DNA binding / nucleus
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #40 / LEM-like domain / Lamina-associated polypeptide 2 alpha, C-terminal / Thymopoietin protein / Lamina-associated polypeptide 2 alpha / LEM-like domain profile. / Thymopoietin / LEM domain / LEM domain / LEM domain profile. ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #40 / LEM-like domain / Lamina-associated polypeptide 2 alpha, C-terminal / Thymopoietin protein / Lamina-associated polypeptide 2 alpha / LEM-like domain profile. / Thymopoietin / 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
Lamina-associated polypeptide 2, isoform alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / RESTRAINED SIMULATED IN TORSION ANGLE SPACE
AuthorsClore, G.M. / Cai, M.
CitationJournal: Embo J. / Year: 2001
Title: Solution structure of the constant region of nuclear envelope protein LAP2 reveals two LEM-domain structures: one binds BAF and the other binds DNA.
Authors: Cai, M. / Huang, Y. / Ghirlando, R. / Wilson, K.L. / Craigie, R. / Clore, G.M.
History
DepositionJun 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LAP2


Theoretical massNumber of molelcules
Total (without water)18,4081
Polymers18,4081
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)1 / 20RESTRAINED REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: Protein LAP2 / LAMIN-ASSOCIATED POLYPEPTIDE 2 / THYMOPOIETIN / ISOFORM ALPHA


Mass: 18407.684 Da / Num. of mol.: 1 / Fragment: N-TERMINAL CONSTANT REGION (RESIDUES 1-168)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: nucleus / Production host: Escherichia coli (E. coli) / References: UniProt: P42166

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1) DOUBLE AND TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN; (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; (3) 3D SEPARATED NOE EXPERIMENTS; (4) ...Text: THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1) DOUBLE AND TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN; (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; (3) 3D SEPARATED NOE EXPERIMENTS; (4) 2D and 3D DOUBLE AND TRIPLE RESONANCE EXPERIMENTS FOR DIPOLAR COUPLING MEASUREMENTS IN LIQUID CRYSTALLINE MEDIUM OF PHAGE PF1.

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Sample preparation

Sample conditionsIonic strength: 50 mM SODIUM PHOSPHATE / pH: 7.2 / Temperature: 308.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DRX600BrukerDRX6006002
Bruker DRX750BrukerDRX7507503

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Processing

NMR softwareName: X-PLOR NIH VERSION (AVAILABLE TO ACADEMIC USERS BY ANONYMOUS FTP AT PORTAL.NIDDK.NIH.GOV IN PUB/CLORE/XPLOR_NIH or AT HTTP://NMR.CIT.NIH.GOV)
Developer: CLORE, KUSZEWSKI AND SCHWIETERS. adapted from Brunger (general XPLOR)
Classification: refinement
RefinementMethod: RESTRAINED SIMULATED IN TORSION ANGLE SPACE / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE (C. SCHWIETERS AND G.M. CLORE. IN PRESS). THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE RESTRAINTS, TORSION ...Details: THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE (C. SCHWIETERS AND G.M. CLORE. IN PRESS). THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE RESTRAINTS, TORSION ANGLE RESTRAINTS, CARBON CHEMICAL SHIFT RESTRAINTS (KUSZEWSKI ET AL. J. MAGN. RESON. SERIES B 106, 92-96 (1995)), THE DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON. 133, 216-221(1998)), THE RADIUs OF GYRATION (KUSZEWSKI ET AL. (1999), AND A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-136). IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. ONLY COORDINATES FOR RESIDUES 1-50 (LAP2-N) and 111-153 (LAP2-C) ARE PROVIDED. THE LINKER CONNECTING THESE TWO DOMAINS IS COMPLETELY DISORDERED. LIKEWISE THE C-TERMINAL RESIDUES (154-168) ARE DISORDERED. SINCE THE TWO DOMAINS, LAP2-N AND LAP2-C, REORIENT ESSENTIALLY INDEPENDENTLY IN SOLUTION, THE COORDINATES OF THE TWO DOMAINS HAVE BEEN BEST-FITTED TO EACH OTHER SINCE THEY ARE STRUCTURALY VERY SIMILAR. THE LAP2-N DOMAIN BINDS DNA. THE LAP2-C DOMAIN BINDS THE BARRIER-TO-AUTOINTEGRATION FACTOR BAF. Structural Statistics: --------------------------------------------------------- LAP2-N LAP2-C --------------------------------------------------------- DEVIATIONS FROM IDEALIZED GEOMETRY: BONDS 0.003 A 0.003 A ANGLES 0.48 DEG 0.54 DEG IMPROPERS 0.49 DEG 0.39 DEG DEVIATIONS FROM EXPT RESTRAINTS (LAP2-N/LAP2-C) NOES (395/401) 0.024 A 0.012 A TORSION ANGLES (151/121) 0.49 DEG 0.13 DEG 13C CHEMICAL SHIFTS (105/91) 0.92 PPM 0.81 PPM DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012): 1DNH (39/34) 6.4% 2.9% 1DCH (36/29) 6.4% 1.9% 1DNC' (24/19) 28.2% 26.2% 2DHNC' (24/20) 30.1% 25.3% % RESIDUES IN MOST FAVORABLE REGION OF RAMACHADRAN MAP 84.1% 89.0% NOTE: THE ALIGNMENT TENSOR FOR LAP2-N and LAP2-C ARE DIFFERENT DUE TO THE FACT THAT THE TWO DOMAINS ARE ORIENTED INDEPENDENTLY BY THE PHAGE LIQUID CRYSTALLINE MEDIUM.
NMR ensembleConformer selection criteria: RESTRAINED REGULARIZED MEAN STRUCTURE
Conformers calculated total number: 20 / Conformers submitted total number: 1

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