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- PDB-2rr6: Solution structure of the leucine rich repeat of human acidic leu... -

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Basic information

Entry
Database: PDB / ID: 2rr6
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 / RDC
Function / homology
Function and homology information


ventricular system development / vasculature development / RNA polymerase binding / roof of mouth development / negative regulation of cell differentiation / inner ear development / positive regulation of protein export from nucleus / activation of cysteine-type endopeptidase activity involved in apoptotic process / nucleosome assembly / histone binding ...ventricular system development / vasculature development / RNA polymerase binding / roof of mouth development / negative regulation of cell differentiation / inner ear development / positive regulation of protein export from nucleus / activation of cysteine-type endopeptidase activity involved in apoptotic process / 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, simulated annealing
Model detailslowest energy, model 1
AuthorsTochio, N. / Umehara, T. / Tsuda, K. / Koshiba, S. / Harada, T. / Watanabe, S. / Tanaka, A. / Kigawa, T. / Yokoyama, S.
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
DepositionMay 25, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: 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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Acidic leucine-rich nuclear phosphoprotein 32 family member B / Acidic protein rich in leucines / Putative HLA-DR-associated protein I-2 / PHAPI2 / Silver- ...Acidic protein rich in leucines / Putative HLA-DR-associated protein I-2 / PHAPI2 / Silver-stainable protein SSP29


Mass: 18842.559 Da / Num. of mol.: 1 / Fragment: residues in UNP 1-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANP32B / Production host: cell-free synthesis (others) / References: UniProt: Q92688

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1322D 1H-15N IPAP HSQC
1432D 1H-15N IPAP HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3mM [U-13C; U-15N] protein-1, 20mM [U-2H] TRIS-2, 100mM sodium chloride-3, 1mM [U-2H] DTT-4, 0.02 % sodium azide-5, 90% H2O/10% D2O90% H2O/10% D2O
20.5mM [U-13C; U-15N] protein-6, 20mM [U-2H] TRIS-7, 100mM sodium chloride-8, 1mM [U-2H] DTT-9, 0.02 % sodium azide-10, 5 % C12E5/n-hexanol-11, 90% H2O/10% D2O90% H2O/10% D2O
30.5mM [U-13C; U-15N] protein-12, 20mM [U-2H] TRIS-13, 100mM sodium chloride-14, 1mM [U-2H] DTT-15, 0.02 % sodium azide-16, 9 % polyacrylamide gel-17, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMprotein-1[U-13C; U-15N]1
20 mMTRIS-2[U-2H]1
100 mMsodium chloride-31
1 mMDTT-4[U-2H]1
0.02 %sodium azide-51
0.5 mMprotein-6[U-13C; U-15N]2
20 mMTRIS-7[U-2H]2
100 mMsodium chloride-82
1 mMDTT-9[U-2H]2
0.02 %sodium azide-102
5 %C12E5/n-hexanol-112
0.5 mMprotein-12[U-13C; U-15N]3
20 mMTRIS-13[U-2H]3
100 mMsodium chloride-143
1 mMDTT-15[U-2H]3
0.02 %sodium azide-163
9 %polyacrylamide gel-173
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
KUJIRAN. Kobayashidata analysis
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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