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- PDB-2odg: Complex of barrier-to-autointegration factor and LEM-domain of emerin -

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Basic information

Entry
Database: PDB / ID: 2odg
TitleComplex of barrier-to-autointegration factor and LEM-domain of emerin
Components
  • Barrier-to-autointegration factor
  • Emerin
KeywordsMEMBRANE PROTEIN / PROTEIN BINDING / INNER NUCLEAR MEMBRANE PROTEIN / LEM-DOMAIN BAF MULTIDIMENSIONAL NMR DIPOLAR COUPLINGS
Function / homology
Function and homology information


TMEM240-body / nuclear membrane organization / negative regulation of protein ADP-ribosylation / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / nuclear outer membrane / regulation of canonical Wnt signaling pathway ...TMEM240-body / nuclear membrane organization / negative regulation of protein ADP-ribosylation / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / nuclear outer membrane / regulation of canonical Wnt signaling pathway / nuclear inner membrane / muscle organ development / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / negative regulation of type I interferon production / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of viral genome replication / negative regulation of cGAS/STING signaling pathway / 2-LTR circle formation / beta-tubulin binding / Vpr-mediated nuclear import of PICs / skeletal muscle cell differentiation / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / RHOG GTPase cycle / chromosome organization / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of fibroblast proliferation / condensed chromosome / RAC1 GTPase cycle / negative regulation of innate immune response / positive regulation of protein export from nucleus / muscle contraction / response to virus / negative regulation of canonical Wnt signaling pathway / cellular response to growth factor stimulus / DNA integration / spindle / chromatin organization / nuclear envelope / actin binding / double-stranded DNA binding / nuclear membrane / microtubule / response to oxidative stress / cadherin binding / chromatin / endoplasmic reticulum / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Emerin, LEM domain / Emerin / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #40 / Barrier-to-autointegration factor, BAF / Barrier- to-autointegration factor, BAF / Barrier-to-autointegration factor, BAF superfamily / Barrier to autointegration factor / Barrier to autointegration factor / LEM domain / LEM domain ...Emerin, LEM domain / Emerin / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #40 / Barrier-to-autointegration factor, BAF / Barrier- to-autointegration factor, BAF / Barrier-to-autointegration factor, BAF superfamily / Barrier to autointegration factor / Barrier to autointegration factor / 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 / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Barrier-to-autointegration factor / Emerin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE SIMULATED ANNEALING DYNAMICS
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. IT IS IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE ATOMS AND NON-INTERFACIAL SIDECHAINS PROVIDE ONLY A MEASURE OF THE PRECISION WITH WHICH THE RELATIVE ORIENTATION OF THE TWO PROTEINS HAVE BEEN DETERMINED AND DOES NOT TAKE INTO ACCOUNT THE ERRORS IN THE NMR COORDINATES OF THE FREE BAF DIMER AND THE LEM-DOMAIN OF EMERIN. STRUCTURAL STATISTICS: --------------------------------------------------------- RMS DEVIATIONS FROM EXPT RESTRAINTS NOES (122) 0.016 A SIDE-CHAIN TORSION ANGLES (46) 0.025 DEG 1DNH DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012): BAF (54x2) 15.2% LEM-DOMAIN: 14.8% -------------------------------------------------------- COORDINATE PRECISION BACKBONE: 0.13(+/-0.06) A INTERFACIAL SIDE-CHAIN HEAVY ATOMS: 1.02(+/-0.02) A

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Barrier-to-autointegration factor
B: Barrier-to-autointegration factor
C: Emerin


Theoretical massNumber of molelcules
Total (without water)25,8683
Polymers25,8683
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 / 180RESTRAINED REGULARIZED MEAN STRUCTURE
RepresentativeModel #1restrained regularized mean coordinates

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Components

#1: Protein Barrier-to-autointegration factor / Breakpoint cluster region protein 1


Mass: 10073.588 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Gene: BANF1, BAF, BCRG1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75531
#2: 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: 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 HETREONUCLEAR-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 200 mM NACL / 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 DRXBrukerDRX7504

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSCHWIETERS, KUSZEWSKI, CLORErefinement
XPLOR-NIHstructure solution
RefinementMethod: CONJOINED RIGID BODY, TORSION ANGLE SIMULATED ANNEALING DYNAMICS
Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302). THE TARGET FUNCTIONS COMPRISES TERMS FOR NOE RESTRAINTS, ...Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302). THE TARGET FUNCTIONS COMPRISES TERMS FOR NOE RESTRAINTS, SIDECHAIN TORSION ANGLE RESTRAINTS, RESIDUAL DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON.133, 216-221(1998)), A RADIUS OF GYRATION TERM (KUSZEWSKI ET AL. J.AM.CHEM.SOC. 121, 2337-2338 (1999)), A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-136), AND A TORSION ANGLE CONFORMATIONAL DATABASE POTENTIAL OF MEAN FORCE (CLORE AND KUSZEWSKI 2002) J.AM.CHEM.SOC 124, 2866-2867). THE STARTING COORDINATE COME FROM THE NMR STRUCTURE OF THE BAF DIMER (1QCK; KUSZEWSKI ET AL. J.AM.CHEM.SOC.121, 2337-2338(1999)) AND THE LEM-DOMAIN OF EMERIN (PDB ID 2ODC; CAI ET AL) THE BACKBONE COORDINATES AND NON-INTERFACIAL SIDECHAINS ARE TREATED AS RIGID BODIES THROUGHOUT WITH THE BAF DIMER HELD FIXED, THE MOLECULES ALLOWED TO ROTATE AND TRANSLATE, AND THE AXIS OF THE SINGLE DIPOLAR COUPLING ALIGNMENT TENSOR FREE TO ROTATE. THE INTERFACIAL SIDECHAINS ARE GIVEN FULL TORSIONAL DEGREES OF FREEDOM.
NMR representativeSelection criteria: restrained regularized mean coordinates
NMR ensembleConformer selection criteria: RESTRAINED REGULARIZED MEAN STRUCTURE
Conformers calculated total number: 180 / Conformers submitted total number: 1

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