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- PDB-2ell: Solution structure of the Leucine Rich Repeat of human Acidic leu... -

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Basic information

Entry
Database: PDB / ID: 2ell
TitleSolution structure of the Leucine Rich Repeat of human Acidic leucine-rich nuclear phosphoprotein 32 family member B
ComponentsAcidic leucine-rich nuclear phosphoprotein 32 family member B
KeywordsGENE REGULATION / PHAPI2 protein / Silver-stainable protein SSP29 / Acidic protein rich in leucines / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


ventricular system development / vasculature development / RNA polymerase binding / roof of mouth development / inner ear development / negative regulation of cell differentiation / positive regulation of protein export from nucleus / : / nucleosome assembly / histone binding ...ventricular system development / vasculature development / RNA polymerase binding / roof of mouth development / inner ear development / negative regulation of cell differentiation / positive regulation of protein export from nucleus / : / nucleosome assembly / histone binding / regulation of apoptotic process / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Acidic leucine-rich nuclear phosphoprotein 32 / Leucine Rich repeats (2 copies) / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat ...Acidic leucine-rich nuclear phosphoprotein 32 / Leucine Rich repeats (2 copies) / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Acidic leucine-rich nuclear phosphoprotein 32 family member B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / Umehara, T. / Tanaka, A. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Solution structure of histone chaperone ANP32B: interaction with core histones H3-H4 through its acidic concave domain.
Authors: Tochio, N. / Umehara, T. / Munemasa, Y. / Suzuki, T. / Sato, S. / Tsuda, K. / Koshiba, S. / Kigawa, T. / Nagai, R. / Yokoyama, S.
History
DepositionMar 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acidic leucine-rich nuclear phosphoprotein 32 family member B


Theoretical massNumber of molelcules
Total (without water)18,8431
Polymers18,8431
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)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Acidic leucine-rich nuclear phosphoprotein 32 family member B / PHAPI2 protein / Silver-stainable protein SSP29 / Acidic protein rich in leucines


Mass: 18842.559 Da / Num. of mol.: 1 / Fragment: LRR_1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: ANP32B / Plasmid: P060227-01 / References: UniProt: Q92688

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.3mM sample U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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