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- PDB-2loo: Backbone structure of human membrane protein TMEM14A from NOE data -

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Basic information

Entry
Database: PDB / ID: 2loo
TitleBackbone structure of human membrane protein TMEM14A from NOE data
ComponentsTransmembrane protein 14A
KeywordsMEMBRANE PROTEIN / helical bundle
Function / homology
Function and homology information


regulation of heme biosynthetic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / mitochondrial membrane / endoplasmic reticulum membrane / negative regulation of apoptotic process / apoptotic process
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1330 / Transmembrane protein 14-like / TMEM14 family / TMEM14 superfamily / Transmembrane proteins 14C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transmembrane protein 14A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsEichmann, C. / Klammt, C. / Maslennikov, I. / Riek, R. / Choe, S.
CitationJournal: Nat.Methods / Year: 2012
Title: Facile backbone structure determination of human membrane proteins by NMR spectroscopy.
Authors: Klammt, C. / Maslennikov, I. / Bayrhuber, M. / Eichmann, C. / Vajpai, N. / Chiu, E.J. / Blain, K.Y. / Esquivies, L. / Kwon, J.H. / Balana, B. / Pieper, U. / Sali, A. / Slesinger, P.A. / ...Authors: Klammt, C. / Maslennikov, I. / Bayrhuber, M. / Eichmann, C. / Vajpai, N. / Chiu, E.J. / Blain, K.Y. / Esquivies, L. / Kwon, J.H. / Balana, B. / Pieper, U. / Sali, A. / Slesinger, P.A. / Kwiatkowski, W. / Riek, R. / Choe, S.
History
DepositionJan 26, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane protein 14A


Theoretical massNumber of molelcules
Total (without water)11,7351
Polymers11,7351
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 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Transmembrane protein 14A


Mass: 11735.306 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM14A, C6orf73, PTD011 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q9Y6G1

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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 HNCA
1323D HN(CA)CB
1413D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
115N-TMEM14A, 20 mM MES-Bis-TRIS, 2 % LMPG, 0.5 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
213C,15N-TMEM14A, 20 mM MES-Bis-TRIS, 2 % LMPG, 0.5 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
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Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMMES-Bis-TRIS-11
2 %LMPG-21
0.5 mMDSS-31
20 mMMES-Bis-TRIS-42
2 %LMPG-52
0.5 mMDSS-62
20 mMMES-Bis-TRIS-73
2 %LMPG-83
0.5 mMDSS-93
Sample conditionsIonic strength: 40 / pH: 6 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7001
Bruker DRXBrukerDRX7002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
PROSAGuntertprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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