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- PDB-5njg: Structure of an ABC transporter: part of the structure that could... -

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Basic information

Entry
Database: PDB / ID: 5njg
TitleStructure of an ABC transporter: part of the structure that could be built de novo
Components
  • 5D3-Fab heavy chain
  • 5D3-Fab light chain
  • ATP-binding cassette sub-family G member 2
KeywordsTRANSPORT PROTEIN / ABC transporter / transport protein
Function / homologyP-loop containing nucleoside triphosphate hydrolase / ABC-2 type transporter / Iron uptake and transport / Abacavir transmembrane transport / ABC-2 type transporter / ATP-binding cassette, ABC transporter-type domain profile. / AAA+ ATPase domain / ABC transporter-like / ATP-binding cassette subfamily G member 2 / ABC transporter ...P-loop containing nucleoside triphosphate hydrolase / ABC-2 type transporter / Iron uptake and transport / Abacavir transmembrane transport / ABC-2 type transporter / ATP-binding cassette, ABC transporter-type domain profile. / AAA+ ATPase domain / ABC transporter-like / ATP-binding cassette subfamily G member 2 / ABC transporter / heme transporter activity / urate metabolic process / xenobiotic transmembrane transporting ATPase activity / cholesterol efflux / ATPase activity, coupled to transmembrane movement of substances / mitochondrial membrane / transporter activity / cellular iron ion homeostasis / receptor complex / apical plasma membrane / response to drug / protein homodimerization activity / integral component of membrane / ATP binding / identical protein binding / plasma membrane / nucleus / ATP-binding cassette sub-family G member 2
Function and homology information
Specimen sourceHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.78 Å resolution
AuthorsTaylor, N.M.I. / Manolaridis, I. / Jackson, S.M. / Kowal, J. / Stahlberg, H. / Locher, K.P.
CitationJournal: Nature / Year: 2017
Title: Structure of the human multidrug transporter ABCG2.
Authors: Nicholas M I Taylor / Ioannis Manolaridis / Scott M Jackson / Julia Kowal / Henning Stahlberg / Kaspar P Locher
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 28, 2017 / Release: Jun 7, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 7, 2017Structure modelrepositoryInitial release
1.1Jun 28, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
1.2Aug 30, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_imaging_optics / em_software_em_3d_fitting.ref_space / _em_imaging_optics.energyfilter_name / _em_software.details / _em_software.name

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-3654
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-binding cassette sub-family G member 2
B: ATP-binding cassette sub-family G member 2
C: 5D3-Fab heavy chain
D: 5D3-Fab light chain
E: 5D3-Fab heavy chain
F: 5D3-Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,55210
Polyers241,6676
Non-polymers8854
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)11380
ΔGint (kcal/M)-54
Surface area (Å2)41970
MethodPISA

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Components

#1: Protein/peptide ATP-binding cassette sub-family G member 2 / Breast cancer resistance protein / CDw338 / Mitoxantrone resistance-associated protein / Placenta-specific ATP-binding cassette transporter / Urate exporter


Mass: 73395.742 Da / Num. of mol.: 2 / Mutation: Has an N-terminal Flag-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ABCG2, ABCP, BCRP, BCRP1, MXR / Cell line (production host): HEK293-EBNA / Production host: Homo sapiens (human) / References: UniProt: Q9UNQ0
#2: Protein/peptide 5D3-Fab heavy chain


Mass: 23843.633 Da / Num. of mol.: 2 / Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#3: Protein/peptide 5D3-Fab light chain


Mass: 23594.016 Da / Num. of mol.: 2 / Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#4: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Nanodisc-reconstituted ABCG2 in complex with 5D3-FabCOMPLEX1, 2, 30MULTIPLE SOURCES
2Nanodisc-reconstituted ABCG2COMPLEX11RECOMBINANT
35D3-FabCOMPLEX2, 31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens (human)
2310090Mus musculus (house mouse)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens (human)
2310090Mus musculus (house mouse)
Buffer solutionpH: 7.5
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 67 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameCategoryDetails
1Gautomatchparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION3D reconstruction
13PHENIXmodel refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 97612 / Symmetry type: POINT
Atomic model buildingRef space: REAL

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