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- PDB-2l8d: Structure/function of the LBR Tudor domain -

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Basic information

Entry
Database: PDB / ID: 2l8d
TitleStructure/function of the LBR Tudor domain
ComponentsLamin-B receptor
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


Delta14-sterol reductase / delta14-sterol reductase activity / neutrophil differentiation / sterol biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors / nuclear inner membrane / cholesterol biosynthetic process / NADPH binding / membrane => GO:0016020 / endoplasmic reticulum membrane ...Delta14-sterol reductase / delta14-sterol reductase activity / neutrophil differentiation / sterol biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors / nuclear inner membrane / cholesterol biosynthetic process / NADPH binding / membrane => GO:0016020 / endoplasmic reticulum membrane / DNA binding / nucleus / cytoplasm
Similarity search - Function
Lamin-B receptor of TUDOR domain / Lamin-B receptor of TUDOR domain / Sterol biosynthesis ERG24/DHCR-like / Sterol reductase, conserved site / Ergosterol biosynthesis ERG4/ERG24 family / Sterol reductase family signature 1. / Sterol reductase family signature 2. / Tudor domain / Tudor domain / SH3 type barrels. - #140 ...Lamin-B receptor of TUDOR domain / Lamin-B receptor of TUDOR domain / Sterol biosynthesis ERG24/DHCR-like / Sterol reductase, conserved site / Ergosterol biosynthesis ERG4/ERG24 family / Sterol reductase family signature 1. / Sterol reductase family signature 2. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Delta(14)-sterol reductase LBR
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsclosest to the average, model 7
AuthorsLiokatis, S. / Edlich, C. / Soupsana, K. / Giannios, I. / Sattler, M. / Georgatos, S.D. / Politou, A.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Solution structure and molecular interactions of lamin B receptor tudor domain.
Authors: Liokatis, S. / Edlich, C. / Soupsana, K. / Giannios, I. / Panagiotidou, P. / Tripsianes, K. / Sattler, M. / Georgatos, S.D. / Politou, A.S.
History
DepositionJan 10, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lamin-B receptor


Theoretical massNumber of molelcules
Total (without water)7,4901
Polymers7,4901
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)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Lamin-B receptor


Mass: 7490.399 Da / Num. of mol.: 1 / Fragment: sequence database residues 1-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LBR / Production host: Escherichia coli (E. coli) / References: UniProt: P23913

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCA
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1823D 1H-13C NOESY aliphatic
1922D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
220 mM sodium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate-11
100 mMsodium chloride-21
20 mMsodium phosphate-32
100 mMsodium chloride-42
Sample conditionsIonic strength: 0.1 / pH: 6.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdihedral angle restraints
ProcheckNMRLaskowski and MacArthurstructure quality analysis
WHAT IFVriendstructure quality analysis
MOLMOLKoradi, Billeter and Wuthrichmolecular images
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
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: 10

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