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- PDB-1p23: STRUCTURE OF THE DIMERIZED CYTOPLASMIC DOMAIN OF P23 IN SOLUTION,... -

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Basic information

Entry
Database: PDB / ID: 1p23
TitleSTRUCTURE OF THE DIMERIZED CYTOPLASMIC DOMAIN OF P23 IN SOLUTION, NMR, 10 STRUCTURES
ComponentsTRANSMEMBRANE PROTEIN TMP21 PRECURSORTransmembrane protein
KeywordsMEMBRANE PROTEIN / TRANSPORT / PROTEIN TRANSPORT / TRANSMEMBRANE / GLYCOPROTEIN / VESICULAR TRANSPORT / COP / COATOMER / GOLGI STACK / SOLUTION STRUCTURE / P24 FAMILY / INTEGRAL MEMBRANE PROTEIN
Function / homology
Function and homology information


COPI-coated vesicle budding / protein localization to ERGIC / cytosol to ERGIC protein transport / regulation of amyloid-beta formation / COPI-coated vesicle / gamma-secretase complex / positive regulation of interleukin-1 production / trans-Golgi network transport vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / transport vesicle membrane ...COPI-coated vesicle budding / protein localization to ERGIC / cytosol to ERGIC protein transport / regulation of amyloid-beta formation / COPI-coated vesicle / gamma-secretase complex / positive regulation of interleukin-1 production / trans-Golgi network transport vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / transport vesicle membrane / protein transmembrane transporter activity / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / positive regulation of protein secretion / melanosome / Golgi membrane / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
emp24/gp25L/p24 family/GOLD / emp24/gp25L/p24 family/GOLD / Transmembrane emp24 domain-containing protein / GOLD domain / GOLD domain profile.
Similarity search - Domain/homology
Transmembrane emp24 domain-containing protein 10
Similarity search - Component
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsWeidler, M. / Reinhard, C. / Wieland, F.T. / Roesch, P.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2000
Title: Structure of the cytoplasmic domain of p23 in solution: implications for the formation of COPI vesicles.
Authors: Weidler, M. / Reinhard, C. / Friedrich, G. / Wieland, F.T. / Rosch, P.
History
DepositionNov 17, 1998Processing site: BNL
Revision 1.0Jun 7, 2000Provider: 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: TRANSMEMBRANE PROTEIN TMP21 PRECURSOR
B: TRANSMEMBRANE PROTEIN TMP21 PRECURSOR
C: TRANSMEMBRANE PROTEIN TMP21 PRECURSOR
D: TRANSMEMBRANE PROTEIN TMP21 PRECURSOR


Theoretical massNumber of molelcules
Total (without water)7,2814
Polymers7,2814
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)10 / 100ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
RepresentativeModel #1

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Components

#1: Protein/peptide
TRANSMEMBRANE PROTEIN TMP21 PRECURSOR / Transmembrane protein / INTEGRAL MEMBRANE PROTEIN P23


Mass: 1820.271 Da / Num. of mol.: 4 / Fragment: CYTOPLASMIC DOMAIN
Source method: isolated from a genetically manipulated source
Details: CHEMICALLY SYNTHESIZED. THE FRAGMENT (CYTOPLASMIC DOMAIN) OCCURS NATURALLY IN NEW ZEALAND WHITE RABBIT'S LIVER(TRANSMEMBRANE PROTEIN TMP21 PRECURSOR).
References: UniProt: Q28735

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Experimental details

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Experiment

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

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Sample preparation

Sample conditionsIonic strength: 650 mM / pH: 3.60 / Pressure: 10E+5 PA atm / Temperature: 280.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

Software
NameVersionClassification
X-PLOR3.84model building
X-PLOR3.84refinement
X-PLOR3.84phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.84BRUNGERrefinement
NDEE2structure solution
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: STRATEGY USED FOR NMR STRUCTURE CALCULATION: EXPERIMENTAL RESTRAINTS FOR THE STRUCTURE CALCULATIONS INITIALLY, FREQUENCY DEGENERATED NOESY CROSS -PEAKS WERE INCORPORATED INTO THE STRUCTURE ...Details: STRATEGY USED FOR NMR STRUCTURE CALCULATION: EXPERIMENTAL RESTRAINTS FOR THE STRUCTURE CALCULATIONS INITIALLY, FREQUENCY DEGENERATED NOESY CROSS -PEAKS WERE INCORPORATED INTO THE STRUCTURE CALCULATION AS 'AMBIGUOUS'. SUBSEQUENTLY, THE PROTON-PROTON DISTANCES IN THE CALCULATED STRUCTURES WERE DETERMINED USING THE PROGRAM 'BACKCALC_DB 2.0' (SOFTWARE SYMBIOSE, INC., BAYREUTH, GERMANY) AND COMPARED WITH THE COMBINATIONS OF DISTANCES POSSIBLE FOR EACH FREQUENCY DEGENERATED NOESY CROSS-PEAK. IF ONLY ONE OF THE POSSIBLE DISTANCE COMBINATIONS WAS FULFILLED IN MORE THAN 50% OF THE CALCULATED STRUCTURES, THE DISTANCE INFORMATION WAS USED IN FURTHER STRUCTURE CALCULATIONS. THIS PROCEDURE WAS REPEATED SEVERAL TIMES, LEADING TO A TOTAL OF 223 INTRARESIDUAL AND 249 INTERRESIDUAL NOE CONNECTIVITIES. STRUCTURE CALCULATIONS STRUCTURES CALCULATIONS WERE PERFORMED USING A MODIFIED AB INITIO SIMULATED ANNEALING PROTOCOL (NILGES, UNPUBLISHED) WITH X-PLOR V3.840. THE CALCULATION STRATEGY INCLUDES FLOATING ASSIGNMENT OF PROCHIRAL GROUPS AND A REDUCED PRESENTATION FOR NON- BONDED INTERACTIONS FOR PART OF THE CALCULATION TO INCREASE EFFICIENCY. A MORE DETAILED DESCRIPTION OF THE PROTOCOL IS GIVEN IN KHARRAT ET AL. (EMBO J. 14 (1995) 3572-84). STRUCTURE PARAMETERS WERE EXTRACTED FROM THE STANDARD FILES PARALLHDG.PRO AND TOPALLHDG.PRO OF X-PLOR V3.840. IN EACH ROUND OF THE STRUCTURE CALCULATION 100 STRUCTURES WERE CALCULATED. OF THE 100 STRUCTURES RESULTING FROM THE FINAL ROUND OF STRUCTURE CALCULATION, THOSE 30 STRUCTURES THAT SHOWED THE LOWEST TOTAL ENERGY VALUES WERE SELECTED FOR FURTHER CHARACTERIZATION.
NMR ensembleConformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 100 / Conformers submitted total number: 10

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