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- PDB-2lom: Backbone structure of human membrane protein HIGD1A -

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Basic information

Entry
Database: PDB / ID: 2lom
TitleBackbone structure of human membrane protein HIGD1A
ComponentsHIG1 domain family member 1A
KeywordsMEMBRANE PROTEIN / Helical bundle
Function / homology
Function and homology information


: / mitochondrial respirasome assembly / : / Regulation of gene expression by Hypoxia-inducible Factor / negative regulation of release of cytochrome c from mitochondria / cellular response to glucose starvation / respirasome / positive regulation of protein serine/threonine kinase activity / mitochondrial inner membrane / membrane => GO:0016020 ...: / mitochondrial respirasome assembly / : / Regulation of gene expression by Hypoxia-inducible Factor / negative regulation of release of cytochrome c from mitochondria / cellular response to glucose starvation / respirasome / positive regulation of protein serine/threonine kinase activity / mitochondrial inner membrane / membrane => GO:0016020 / negative regulation of apoptotic process / protein-containing complex / mitochondrion / nucleoplasm
Similarity search - Function
Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile.
Similarity search - Domain/homology
HIG1 domain family member 1A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsBlain, K. / Klammt, C. / Maslennikov, I. / Kwiatkowski, W. / 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 / pdbx_nmr_software
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
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: HIG1 domain family member 1A


Theoretical massNumber of molelcules
Total (without water)10,1571
Polymers10,1571
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)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein HIG1 domain family member 1A / Hypoxia-inducible gene 1 protein


Mass: 10156.917 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIGD1A, HIG1, HSPC010 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q9Y241

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1142D 1H-15N HSQC
1242D HNCO
1333D HNCO
1433D HNCA
1533D HN(CA)CB
1613D 1H-15N NOESY
1723D 13C-15N HSQC-NOESY-HSQC
1812D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
115N-HIGD1A, 20 mM MES-Bis-TRIS, 2 % LMPG, 95% H2O/5% D2O95% H2O/5% D2O
213C,15N-HIGD1A, 20 mM MES-Bis-TRIS, 2 % LMPG, 95% H2O/5% D2O95% H2O/5% D2O
313C,15N-HIGD1A, 20 mM MES-Bis-TRIS, 2 % LMPG, 95% H2O/5% D2O95% H2O/5% D2O
413C(1),15N-Selectively labeled-HIGD1A, 20 mM MES-Bis-TRIS, 2 % LMPG, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMMES-Bis-TRIS-11
2 %LMPG-21
20 mMMES-Bis-TRIS-32
2 %LMPG-42
20 mMMES-Bis-TRIS-53
2 %LMPG-63
20 mMMES-Bis-TRIS-74
2 %LMPG-84
20 mMMES-Bis-TRIS-95
2 %LMPG-105
20 mMMES-Bis-TRIS-116
2 %LMPG-126
Sample conditionsIonic strength: 40 / pH: 6.0 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.04Guntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection
MCCL1(MCCL) Kwiatkowski, Maslennikovcombinatorial chemical shift assignment
MCCL1(MCCL) Kwiatkowski, Maslennikovdata analysis
CARAKeller and Wuthrichchemical shift assignment
CARAKeller 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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