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- PDB-2mof: Structural insights of TM domain of LAMP-2A in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2mof
TitleStructural insights of TM domain of LAMP-2A in DPC micelles
ComponentsLysosome-associated membrane glycoprotein 2
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


chaperone-mediated autophagy translocation complex / lysosomal protein catabolic process / platelet dense granule membrane / protein targeting to lysosome involved in chaperone-mediated autophagy / negative regulation of NLRP3 inflammasome complex assembly / lysosomal lumen acidification / protein import / autolysosome / azurophil granule membrane / ion channel inhibitor activity ...chaperone-mediated autophagy translocation complex / lysosomal protein catabolic process / platelet dense granule membrane / protein targeting to lysosome involved in chaperone-mediated autophagy / negative regulation of NLRP3 inflammasome complex assembly / lysosomal lumen acidification / protein import / autolysosome / azurophil granule membrane / ion channel inhibitor activity / chaperone-mediated autophagy / muscle cell cellular homeostasis / autophagosome membrane / autophagosome maturation / ficolin-1-rich granule membrane / protein targeting / negative regulation of protein-containing complex assembly / signaling adaptor activity / cellular response to starvation / lysosomal lumen / trans-Golgi network / regulation of protein stability / protein catabolic process / Chaperone Mediated Autophagy / phagocytic vesicle membrane / late endosome / Platelet degranulation / late endosome membrane / lysosome / protein stabilization / protein domain specific binding / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / perinuclear region of cytoplasm / enzyme binding / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / : / Lysosome-associated membrane glycoprotein 2, transmembrane segment / Lysosome-associated membrane glycoprotein, conserved site / Lysosome-associated membrane glycoproteins duplicated domain signature. / LAMP glycoproteins transmembrane and cytoplasmic domain signature. / Lysosome-associated membrane glycoprotein / Lysosome-associated membrane glycoprotein 2-like, luminal domains / Lysosome-associated membrane glycoprotein family profile.
Similarity search - Domain/homology
Lysosome-associated membrane glycoprotein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsTjandra, N. / Rout, A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure of Transmembrane Domain of Lysosome-associated Membrane Protein Type 2a (LAMP-2A) Reveals Key Features for Substrate Specificity in Chaperone-mediated Autophagy.
Authors: Rout, A.K. / Strub, M.P. / Piszczek, G. / Tjandra, N.
History
DepositionApr 25, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2May 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysosome-associated membrane glycoprotein 2


Theoretical massNumber of molelcules
Total (without water)4,4841
Polymers4,4841
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Lysosome-associated membrane glycoprotein 2 / LAMP-2 / Lysosome-associated membrane protein 2 / CD107 antigen-like family member B


Mass: 4484.159 Da / Num. of mol.: 1 / Fragment: unp residues 369-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13473

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCO
1323D HNCA
1423D HN(CO)CA
1523D CBCA(CO)NH
1623D HN(CA)CB
1713D 1H-15N NOESY
1834D (H)CCH NOESY
1933D 13C Filter NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-99% 15N] TM domain of LAMP2A, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-99% 13C; U-99% 15N] TM domain of LAMP2A, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM [U-99% 13C; U-99% 15N] TM domain of LAMP2A, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMTM domain of LAMP2A-1[U-99% 15N]1
0.6 mMTM domain of LAMP2A-2[U-99% 13C; U-99% 15N]2
0.6 mMTM domain of LAMP2A-3[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 25 / pH: 6.3 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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