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- PDB-2mx7: Solution structure of the internal EH domain of gamma-synergin -

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Basic information

Entry
Database: PDB / ID: 2mx7
TitleSolution structure of the internal EH domain of gamma-synergin
ComponentsSynergin gamma
KeywordsPROTEIN BINDING / EH domain / EF hand / NPF repeat
Function / homology
Function and homology information


clathrin coat of trans-Golgi network vesicle / AP-1 adaptor complex / intracellular protein transport / endocytosis / perinuclear region of cytoplasm / Golgi apparatus / cytoplasm
Similarity search - Function
Synergin gamma / EH domain / EH domain profile. / Eps15 homology domain / EH domain / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKovermann, M. / Weininger, U. / Loew, C.
CitationJournal: To be Published
Title: Solution structure of the internal EH domain of gamma-synergin
Authors: Kovermann, M. / Weininger, U. / Loew, C.
History
DepositionDec 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1May 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: Synergin gamma


Theoretical massNumber of molelcules
Total (without water)12,2941
Polymers12,2941
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)10 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Synergin gamma / AP1 subunit gamma-binding protein 1 / Gamma-synergin


Mass: 12294.267 Da / Num. of mol.: 1 / Fragment: internal EH domain (UNP residues 279-388)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNRG, AP1GBP1, SYNG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UMZ2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D HN(COCA)CB
11113D (H)CCH-TOCSY
11212D 1H-15N HSQC IPAP

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] protein, 20 mM TRIS, 100 mM sodium chloride, 2 mM calcium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-99% 13C; U-99% 15N]1
20 mMTRIS-21
100 mMsodium chloride-31
2 mMcalcium chloride-41
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8502

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1575 / Protein phi angle constraints total count: 93 / Protein psi angle constraints total count: 92
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 10

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