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- PDB-6hbu: Cryo-EM structure of the ABCG2 E211Q mutant bound to ATP and Magnesium -

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Basic information

Entry
Database: PDB / ID: 6hbu
TitleCryo-EM structure of the ABCG2 E211Q mutant bound to ATP and Magnesium
ComponentsATP-binding cassette sub-family G member 2
KeywordsMEMBRANE PROTEIN / Multidrug transporter / membrane protein / cancer
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 / transporter activity / mitochondrial membrane / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.09 Å resolution
AuthorsManolaridis, I. / Jackson, S.M. / Taylor, N.M.I. / Kowal, J. / Stahlberg, H. / Locher, K.P.
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structures of a human ABCG2 mutant trapped in ATP-bound and substrate-bound states
Authors: Manolaridis, I. / Jackson, S.M. / Taylor, N.M.I. / Kowal, J. / Stahlberg, H. / Locher, K.P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 13, 2018 / Release: Nov 7, 2018

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Structure visualization

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8336
Polyers144,7702
Non-polymers1,0634
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)11050
ΔGint (kcal/M)-89
Surface area (Å2)44040
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: 72384.867 Da / Num. of mol.: 2 / Mutation: E211Q / 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: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium

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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
1inhibitor-bound ABCG2COMPLEX10MULTIPLE SOURCES
2A mutant (E211Q) of the ATP-binding cassette sub-family G member 2COMPLEX11RECOMBINANT
Source (natural)Organism: HOMO SAPIENS (human)
Source (recombinant)Organism: HOMO SAPIENS (human)
Buffer solutionpH: 7.5
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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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 / Nominal magnification: 165000
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 4905

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
12RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 288447 / Symmetry type: POINT
Atomic model buildingOverall b value: 136
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0099339
ELECTRON MICROSCOPYf_angle_d1.13612652
ELECTRON MICROSCOPYf_dihedral_angle_d7.8345526
ELECTRON MICROSCOPYf_chiral_restr0.0601466
ELECTRON MICROSCOPYf_plane_restr0.0071566

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