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- PDB-7l6k: ApoL1 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7l6k
TitleApoL1 N-terminal domain
ComponentsApolipoprotein L1
KeywordsMEMBRANE PROTEIN / Ion channel / kidney disease / lipoprotein
Function / homology
Function and homology information


lipoprotein metabolic process / very-low-density lipoprotein particle / high-density lipoprotein particle / lipid transport / chloride channel activity / cytolysis by host of symbiont cells / Scavenging of heme from plasma / chloride transmembrane transport / cholesterol metabolic process / Post-translational protein phosphorylation ...lipoprotein metabolic process / very-low-density lipoprotein particle / high-density lipoprotein particle / lipid transport / chloride channel activity / cytolysis by host of symbiont cells / Scavenging of heme from plasma / chloride transmembrane transport / cholesterol metabolic process / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood microparticle / endoplasmic reticulum lumen / innate immune response / lipid binding / extracellular space / extracellular region / membrane
Similarity search - Function
Apolipoprotein L / Apolipoprotein L
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHolliday, M.J. / Ultsch, M. / Moran, P. / Fairbrother, W.J. / Kirchhofer, D.
CitationJournal: Commun Biol / Year: 2021
Title: Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif.
Authors: Ultsch, M. / Holliday, M.J. / Gerhardy, S. / Moran, P. / Scales, S.J. / Gupta, N. / Oltrabella, F. / Chiu, C. / Fairbrother, W. / Eigenbrot, C. / Kirchhofer, D.
History
DepositionDec 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
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: Apolipoprotein L1


Theoretical massNumber of molelcules
Total (without water)13,3091
Polymers13,3091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8160 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Apolipoprotein L1 / / Apolipoprotein L / ApoL / Apolipoprotein L-I / ApoL-I


Mass: 13309.070 Da / Num. of mol.: 1 / Fragment: residues 61-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOL1, APOL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14791

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
1121isotropic12D 1H-13C TROSY aromatic
1131isotropic12D 1H-13C HSQC
121isotropic13D HN(CA)CB
1191isotropic23D HNCA
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
1141isotropic23D HNCO
151isotropic13D HN(CA)CO
1151isotropic23D HN(CA)CO
1111isotropic13D (H)CC(CO)NH
1101isotropic13D 1H-15N NOESY
191isotropic13D (H)CCH-TOCSY
1161isotropic13D 1H-13C NOESY aliphatic
1171isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.9 mM [U-99% 13C; U-99% 15N] ApoL1 (61-172), 93% H2O/7% D2O
Details: 0.9 mM 13C15N APOL1 61-172 / Label: 13C15N_sample / Solvent system: 93% H2O/7% D2O
SampleConc.: 0.9 mM / Component: ApoL1 (61-172) / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: 25 mM MES, 25 mM NaCl, 1 mM EDTA, pH 5.5 / Ionic strength: 50 mM / Label: conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
Refinement
MethodSoftware ordinal
simulated annealing2
simulated annealing1
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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