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- PDB-9gi8: Solution structure of homodimeric TMEM106B -

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Basic information

Entry
Database: PDB / ID: 9gi8
TitleSolution structure of homodimeric TMEM106B
ComponentsTransmembrane protein 106B
KeywordsMEMBRANE PROTEIN / Zinc-binding / lysosomal / N-terminal cytoplasmic domain
Function / homology
Function and homology information


lysosomal protein catabolic process / lysosomal lumen acidification / regulation of lysosome organization / lysosome localization / positive regulation of dendrite development / lysosomal transport / lysosome organization / dendrite morphogenesis / neuron cellular homeostasis / late endosome membrane ...lysosomal protein catabolic process / lysosomal lumen acidification / regulation of lysosome organization / lysosome localization / positive regulation of dendrite development / lysosomal transport / lysosome organization / dendrite morphogenesis / neuron cellular homeostasis / late endosome membrane / ATPase binding / lysosome / endosome / lysosomal membrane / plasma membrane
Similarity search - Function
Transmembrane protein 106 / : / : / TM106 protein C-terminal domain / Transmembrane protein 106 N-terminal region
Similarity search - Domain/homology
Transmembrane protein 106B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSchweimer, K. / Perez-Borrajero, C. / Hennig, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HE7291 Germany
CitationJournal: To Be Published
Title: Zinc-mediated regulation of TMEM106B function in the endolysosomal pathway revealed through systematic identification of TRIM2/3 ubiquitination substrates
Authors: Perez-Borrajero, C. / Hennig, J.
History
DepositionAug 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane protein 106B
B: Transmembrane protein 106B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7593
Polymers8,6942
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Transmembrane protein 106B


Mass: 4346.910 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: TMEM106B(54-92) is a synthetic peptide comprising residues 54-92 of TMEM106B
Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NUM4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DQF-COSY
121isotropic22D 1H-1H TOCSY
131isotropic32D 1H-1H NOESY
141isotropic32D 1H-13C HSQC
152isotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM NA TMEM106B(54-92), 3 mM NA ZINC ION, 20 mM NA sodium phosphate, 100 mM NA sodium chloride, 0.5 mM NA TCEP, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution21.8 mM NA TMEM106B(54-92), 5 mM NA ZINC ION, 20 mM NA sodium phosphate, 100 mM NA sodium chloride, 0.5 mM NA TCEP, 90% H2O/10% D2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMTMEM106B(54-92)NA1
3 mMZINC IONNA1
20 mMsodium phosphateNA1
100 mMsodium chlorideNA1
0.5 mMTCEPNA1
1.8 mMTMEM106B(54-92)NA2
5 mMZINC IONNA2
20 mMsodium phosphateNA2
100 mMsodium chlorideNA2
0.5 mMTCEPNA2
Sample conditionsIonic strength: 120 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD6001equipped with CryoProbe
Bruker AVANCE III HDBrukerAVANCE III HD7002
Bruker AVANCE III HDBrukerAVANCE III HD10003equipped with CryoProbe

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.15Guntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJOneMoon Scientificchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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