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- PDB-2l9n: Structure of the human Shwachman-Bodian-Diamond syndrome (SBDS) p... -

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Basic information

Entry
Database: PDB / ID: 2l9n
TitleStructure of the human Shwachman-Bodian-Diamond syndrome (SBDS) protein
ComponentsRibosome maturation protein SBDS
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


leukocyte chemotaxis / bone marrow development / inner cell mass cell proliferation / bone mineralization / hematopoietic progenitor cell differentiation / mitotic spindle organization / cytosolic ribosome assembly / spindle pole / rRNA processing / ribosome binding ...leukocyte chemotaxis / bone marrow development / inner cell mass cell proliferation / bone mineralization / hematopoietic progenitor cell differentiation / mitotic spindle organization / cytosolic ribosome assembly / spindle pole / rRNA processing / ribosome binding / microtubule binding / rRNA binding / nucleolus / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
SBDS protein C-terminal domain, subdomain 1 / Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A; / Ribosome maturation protein SBDS, N-terminal domain / Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, C-terminal domain / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / SBDS protein, domain II ...SBDS protein C-terminal domain, subdomain 1 / Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A; / Ribosome maturation protein SBDS, N-terminal domain / Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, C-terminal domain / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / SBDS protein, domain II / Uncharacterized protein family UPF0023 signature. / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Ribosome maturation protein Sdo1/SBDS-like / Shwachman-Bodian-Diamond syndrome (SBDS) protein / Alpha-Beta Plaits - #240 / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosome maturation protein SBDS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsHilcenko, C. / Freund, S.M.V. / Warren, A.J.
CitationJournal: Genes Dev. / Year: 2011
Title: Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome.
Authors: Finch, A.J. / Hilcenko, C. / Basse, N. / Drynan, L.F. / Goyenechea, B. / Menne, T.F. / Gonzalez Fernandez, A. / Simpson, P. / D'Santos, C.S. / Arends, M.J. / Donadieu, J. / Bellanne- ...Authors: Finch, A.J. / Hilcenko, C. / Basse, N. / Drynan, L.F. / Goyenechea, B. / Menne, T.F. / Gonzalez Fernandez, A. / Simpson, P. / D'Santos, C.S. / Arends, M.J. / Donadieu, J. / Bellanne-Chantelot, C. / Costanzo, M. / Boone, C. / McKenzie, A.N. / Freund, S.M. / Warren, A.J.
History
DepositionFeb 21, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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: Ribosome maturation protein SBDS


Theoretical massNumber of molelcules
Total (without water)28,9581
Polymers28,9581
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribosome maturation protein SBDS / Shwachman-Bodian-Diamond syndrome protein


Mass: 28957.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-97, SBDS / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q9Y3A5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HNCO
1313D HN(CO)CA
1413D HBHA(CO)NH
1513D HN(CA)CB
1613D HN(CA)CO
1713D HNCA
1813D HNCO
1913D HN(CO)CA
11013D HBHA(CO)NH
11113D HN(CA)CB
11213D HN(CA)CO
11312D 1H-15N HSQC
11413D 1H-15N NOESY
11513D 1H-13C NOESY
11612D 1H-13C HSQC
11713D (H)CCH-TOCSY
11813D (H)CCH-COSY
11913D HN(CAN)NH
12013D (H)CC(CO)NH
12113D H(CCCO)NH

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Sample preparation

DetailsContents: 25 mM potassium phosphate, 150 mM sodium chloride, 1 mM DTT, 0.05 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMpotassium phosphate-11
150 mMsodium chloride-21
1 mMDTT-31
0.05 %sodium azide-41
25 mMpotassium phosphate-52
150 mMsodium chloride-62
1 mMDTT-72
0.05 %sodium azide-82
25 mMpotassium phosphate-93
150 mMsodium chloride-103
1 mMDTT-113
0.05 %sodium azide-123
25 mMpotassium phosphate-134
150 mMsodium chloride-144
1 mMDTT-154
0.05 %sodium azide-164
25 mMpotassium phosphate-175
150 mMsodium chloride-185
1 mMDTT-195
0.05 %sodium azide-205
25 mMpotassium phosphate-216
150 mMsodium chloride-226
1 mMDTT-236
0.05 %sodium azide-246
Sample conditionsIonic strength: 0.163 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker DRXBrukerDRX9002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3Goddardchemical shift assignment
Sparky3Goddardpeak picking
TopSpin2.1Bruker Biospinprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 4027 / NOE intraresidue total count: 1490 / NOE long range total count: 822 / NOE medium range total count: 596 / NOE sequential total count: 1119
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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