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- PDB-1neb: SH3 DOMAIN FROM HUMAN NEBULIN, NMR, MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1neb
TitleSH3 DOMAIN FROM HUMAN NEBULIN, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsNEBULIN
KeywordsSH3 DOMAIN / NEBULIN / Z-DISK ASSEMBLY / ACTIN-BINDING
Function / homology
Function and homology information


cardiac muscle thin filament assembly / regulation of actin filament length / somatic muscle development / Striated Muscle Contraction / muscle organ development / structural constituent of muscle / Z disc / actin filament binding / actin cytoskeleton / extracellular exosome / cytosol
Similarity search - Function
Nebulin-like / Nebulin, SH3 domain / Nebulin repeat / Nebulin repeat / Nebulin repeat profile. / NEBU / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. ...Nebulin-like / Nebulin, SH3 domain / Nebulin repeat / Nebulin repeat / Nebulin repeat profile. / NEBU / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsPolitou, A.S. / Pastore, A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: SH3 in muscles: solution structure of the SH3 domain from nebulin.
Authors: Politou, A.S. / Millevoi, S. / Gautel, M. / Kolmerer, B. / Pastore, A.
History
DepositionAug 7, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEBULIN


Theoretical massNumber of molelcules
Total (without water)6,6141
Polymers6,6141
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)1 / 100LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein NEBULIN /


Mass: 6614.411 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-[PLYSS] / References: UniProt: P20929

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY

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Sample preparation

Sample conditionspH: 6.9 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AMXBrukerAMX6002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
BRUKER UXNMRUXNMRstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 / Details: REFINEMENT DETAILS ARE IN THE SUBMITTED PAPER.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 1

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