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- PDB-6hco: Cryo-EM structure of the ABCG2 E211Q mutant bound to estrone 3-su... -

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Basic information

Entry
Database: PDB / ID: 6hco
TitleCryo-EM structure of the ABCG2 E211Q mutant bound to estrone 3-sulfate and 5D3-Fab
Components
  • 5D3-Fab heavy chain
  • 5D3-Fab light chain
  • ATP-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)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.58 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 15, 2018 / Release: Nov 7, 2018

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)242,90011
Polyers241,6656
Non-polymers1,2355
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)12440
ΔGint (kcal/M)-61
Surface area (Å2)64230
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: 73394.758 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: 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)
#3: 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)
#4: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine
#5: Chemical ChemComp-FY5 / estrone 3-sulfate


Mass: 350.429 Da / Num. of mol.: 1 / Formula: C18H22O5S / Estrone sulfate

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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-reconsituted ABCG2 E211Q mutant bound to estrone 3-sulfate and 5D3-FabCOMPLEX1, 2, 30NATURAL
2ABCG2 E211Q mutantCOMPLEX11RECOMBINANT
35D3-FabCOMPLEX2, 31RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
229606Homo sapiens (human)
1310090Mus musculus (house mouse)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganismCell
1310090Mus musculus (house mouse)
229606Homo sapiens (human)HEK293 EBNA
Buffer solutionpH: 7.5
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 100 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 3984
Image scansMovie frames/image: 50

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
7Cootmodel fitting
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 42790 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00912625
ELECTRON MICROSCOPYf_angle_d1.01017121
ELECTRON MICROSCOPYf_dihedral_angle_d7.4467392
ELECTRON MICROSCOPYf_chiral_restr0.0591958
ELECTRON MICROSCOPYf_plane_restr0.0072132

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