[English] 日本語
Yorodumi
- PDB-2kdo: Structure of the human Shwachman-Bodian-Diamond syndrome protein, SBDS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kdo
TitleStructure of the human Shwachman-Bodian-Diamond syndrome protein, SBDS
ComponentsRibosome maturation protein SBDS
KeywordsRNA BINDING PROTEIN / SBDS protein / NMR protein structure / RNA-interacting protein / Disease mutation / Phosphoprotein / Ribosome biogenesis
Function / homology
Function and homology information


leukocyte chemotaxis / bone marrow development / inner cell mass cell proliferation / bone mineralization / hematopoietic progenitor cell differentiation / cytosolic ribosome assembly / mitotic spindle organization / spindle pole / rRNA processing / ribosome binding ...leukocyte chemotaxis / bone marrow development / inner cell mass cell proliferation / bone mineralization / hematopoietic progenitor cell differentiation / cytosolic ribosome assembly / mitotic spindle organization / spindle pole / rRNA processing / ribosome binding / microtubule binding / rRNA binding / nucleolus / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
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 / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, C-terminal domain / 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 / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, domain II / SBDS protein, C-terminal domain / Uncharacterized protein family UPF0023 signature. / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Shwachman-Bodian-Diamond syndrome (SBDS) N-terminal domain / 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 / DGSA-distance geometry simulated annealing, torsion angle dynamics
Model detailsclosest to the average, model 1
Authorsde Oliveira, J.F. / Sforca, M.L. / Blumenschein, T. / Guimaraes, B.G. / Zanchin, N.I.T. / Zeri, A.C.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure, dynamics, and RNA interaction analysis of the human SBDS protein.
Authors: de Oliveira, J.F. / Sforca, M.L. / Blumenschein, T.M. / Goldfeder, M.B. / Guimaraes, B.G. / Oliveira, C.C. / Zanchin, N.I. / Zeri, A.C.
History
DepositionJan 14, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribosome maturation protein SBDS


Theoretical massNumber of molelcules
Total (without water)29,0091
Polymers29,0091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

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


Mass: 29008.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SBDS, CGI-97 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3A5

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HNCA
1413D HN(CO)CA
1513D HNCO
1623D 1H-15N NOESY
1733D (H)CCH-TOCSY
1833D 1H-13C NOESY
1923D 1H-15N TOCSY
11022D 1H-15N HSQC T1
11122D 1H-15N HSQC T1
11222D 1H-15N HSQC T2
11322D 1H-15N HSQC T2
11422D 1H-15N HSQC NOE
11522D 1H-15N HSQC NOE

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N; U-80% 2H] SBDS-1, 1.0 mM no DTT-2, 50 mM no sodium phosphate-3, 20 mM no sodium chloride-4, 0.05 % no sodium azide-5, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-99% 13C; U-99% 15N] SBDS-6, 1.0 mM no DTT-7, 50 mM no sodium phosphate-8, 20 mM no sodium chloride-9, 0.05 % no sodium azide-10, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-99% 13C; U-99% 15N] SBDS-11, 1.0 mM no DTT-12, 50 mM no sodium phosphate-13, 20 mM no sodium chloride-14, 0.05 % no sodium azide-15, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMSBDS-1[U-100% 13C; U-100% 15N; U-80% 2H]1
1.0 mMDTT-2no1
50 mMsodium phosphate-3no1
20 mMsodium chloride-4no1
0.05 %sodium azide-5no1
0.5 mMSBDS-6[U-99% 13C; U-99% 15N]2
1.0 mMDTT-7no2
50 mMsodium phosphate-8no2
20 mMsodium chloride-9no2
0.05 %sodium azide-10no2
0.5 mMSBDS-11[U-99% 13C; U-99% 15N]3
1.0 mMDTT-12no3
50 mMsodium phosphate-13no3
20 mMsodium chloride-14no3
0.05 %sodium azide-15no3
Sample conditionsIonic strength: 0.071 / pH: 7.2 / Pressure: ambient atm / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5Johnson, One Moon Scientificchemical shift assignment
NMRView5Johnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
DYANAGuntert, Braun and Wuthrichstructure solution
DYANAGuntert, Braun and Wuthrichgeometry optimization
Insight IIAccelrys Software Inc.data analysis
ProcheckNMRLaskowski and MacArthurdata analysis
CYANA2.1GUNTERT, P., ET ALrefinement
CNS1.1BRUNGER, A.T. ET ALrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, torsion angle dynamics
Software ordinal: 1
Details: B-FACTOR COLUMN STORES ADDITIONAL COORDINATE DIGITS
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more