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- PDB-1mph: PLECKSTRIN HOMOLOGY DOMAIN FROM MOUSE BETA-SPECTRIN, NMR, 50 STRU... -

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Basic information

Entry
Database: PDB / ID: 1mph
TitlePLECKSTRIN HOMOLOGY DOMAIN FROM MOUSE BETA-SPECTRIN, NMR, 50 STRUCTURES
ComponentsBETA SPECTRIN
KeywordsSIGNAL TRANSDUCTION / INOSITOL PHOSPHATES
Function / homology
Function and homology information


Interaction between L1 and Ankyrins / regulation of SMAD protein signal transduction / RHOV GTPase cycle / membrane assembly / RHOU GTPase cycle / central nervous system formation / NCAM signaling for neurite out-growth / cuticular plate / spectrin / COPI-mediated anterograde transport ...Interaction between L1 and Ankyrins / regulation of SMAD protein signal transduction / RHOV GTPase cycle / membrane assembly / RHOU GTPase cycle / central nervous system formation / NCAM signaling for neurite out-growth / cuticular plate / spectrin / COPI-mediated anterograde transport / RAF/MAP kinase cascade / plasma membrane organization / Golgi to plasma membrane protein transport / actin filament capping / M band / ankyrin binding / cortical actin cytoskeleton / cortical cytoskeleton / mitotic cytokinesis / axolemma / endomembrane system / positive regulation of interleukin-2 production / central nervous system development / cell projection / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / structural constituent of cytoskeleton / phospholipid binding / actin filament binding / cell junction / GTPase binding / actin cytoskeleton organization / postsynapse / postsynaptic density / calmodulin binding / glutamatergic synapse / protein-containing complex binding / nucleolus / protein-containing complex / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats ...Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Spectrin beta chain, non-erythrocytic 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsNilges, M. / Macias, M.J. / O'Donoghue, S.I. / Oschkinat, H.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin.
Authors: Nilges, M. / Macias, M.J. / O'Donoghue, S.I. / Oschkinat, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Molecular Replacement with NMR Models Using Distance-Derived Pseudo B Factors
Authors: Wilmanns, M. / Nilges, M.
#2: Journal: Embo J. / Year: 1995
Title: Structure of the Binding Site for Inositol Phosphates in a Ph Domain
Authors: Hyvonen, M. / Macias, M.J. / Nilges, M. / Oschkinat, H. / Saraste, M. / Wilmanns, M.
#3: Journal: Nature / Year: 1994
Title: Structure of the Pleckstrin Homology Domain from Beta-Spectrin
Authors: Macias, M.J. / Musacchio, A. / Ponstingl, H. / Nilges, M. / Saraste, M. / Oschkinat, H.
History
DepositionApr 23, 1997Processing site: BNL
Revision 1.0Jun 16, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA SPECTRIN


Theoretical massNumber of molelcules
Total (without water)12,2881
Polymers12,2881
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)50 / 200LOWEST ENERGY
Representative

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Components

#1: Protein BETA SPECTRIN / PH DOMAIN


Mass: 12287.853 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Organ: BRAIN / Plasmid: PET21D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q62261

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
1313D TOCSY-NOESY

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
ARIAstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURES WERE CALCULATED WITH A MODIFIED VERSION OF X-PLOR (SEE JRNL REFERENCE FOR DETAILS) WITH A SIMULATED ANNEALING PROTOCOL. AN AUTOMATED PROCEDURE (ARIA) WAS USED TO AUTOMATICALLY ...Details: STRUCTURES WERE CALCULATED WITH A MODIFIED VERSION OF X-PLOR (SEE JRNL REFERENCE FOR DETAILS) WITH A SIMULATED ANNEALING PROTOCOL. AN AUTOMATED PROCEDURE (ARIA) WAS USED TO AUTOMATICALLY ASSIGN AND AUGMENT AN INITIAL LIST OF 568 MANUALLY SELECTED RESTRAINTS, FROM PEAK LISTS FROM TWO H2O NOESY SPECTRA (30 AND 80 MS). 20 STRUCTURES WERE ITERATIVELY REFINED, AND THE NOE DATA RE-ASSIGNED ON THE BASIS OF THE 7 LOWEST ENERGY STRUCTURES IN EACH ITERATION. EIGHT REFINEMENT/ASSIGNMENT CYCLES WERE RUN, PLUS TWO IN AN EXPLICIT SHELL OF WATER. THE FINAL LIST OF RESTRAINTS CONTAINED 1328 UNAMBIGUOUS RESTRAINTS AND 486 AMBIGUOUS RESTRAINTS WITH MAXIMALLY 5 ASSIGNMENT POSSIBILITIES.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 50

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