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- PDB-6hij: Cryo-EM structure of the human ABCG2-MZ29-Fab complex with choles... -

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Basic information

Entry
Database: PDB / ID: 6hij
TitleCryo-EM structure of the human ABCG2-MZ29-Fab complex with cholesterol and PE lipids docked
ComponentsATP-binding cassette sub-family G member 2
KeywordsTRANSPORT PROTEIN / ABC transporter / transport protein
Function / homologyABC transporter-like / Iron uptake and transport / Abacavir transmembrane transport / ATP-binding cassette, ABC transporter-type domain profile. / ABC-2 type transporter / ABC transporter / ATP-binding cassette subfamily G member 2 / P-loop containing nucleoside triphosphate hydrolase / ABC-2 type transporter / AAA+ ATPase domain ...ABC transporter-like / Iron uptake and transport / Abacavir transmembrane transport / ATP-binding cassette, ABC transporter-type domain profile. / ABC-2 type transporter / ABC transporter / ATP-binding cassette subfamily G member 2 / P-loop containing nucleoside triphosphate hydrolase / ABC-2 type transporter / AAA+ ATPase domain / heme transporter activity / urate metabolic process / xenobiotic transmembrane transporting ATPase activity / ATPase activity, coupled to transmembrane movement of substances / transporter activity / mitochondrial membrane / cellular iron ion homeostasis / transmembrane transport / 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 / 3.56 Å resolution
AuthorsJackson, S.M. / Manolaridis, I. / Kowal, J. / Zechner, M. / Taylor, N.M.I. / Bause, M. / Bauer, S. / Bartholomaeus, R. / Stahlberg, H. / Bernhardt, G. / Koenig, B. / Buschauer, A. / Altmann, K.H. / Locher, K.P.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis of small-molecule inhibition of human multidrug transporter ABCG2.
Authors: Scott M Jackson / Ioannis Manolaridis / Julia Kowal / Melanie Zechner / Nicholas M I Taylor / Manuel Bause / Stefanie Bauer / Ruben Bartholomaeus / Guenther Bernhardt / Burkhard Koenig / Armin Buschauer / Henning Stahlberg / Karl-Heinz Altmann / Kaspar P Locher
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 30, 2018 / Release: Sep 19, 2018

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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)155,67822
Polyers144,7722
Non-polymers10,90620
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)19670
ΔGint (kcal/M)-145
Surface area (Å2)46510
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: 72385.852 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: ABCG2, ABCP, BCRP, BCRP1, MXR / Production host: Homo sapiens (human) / References: UniProt: Q9UNQ0
#2: Chemical
ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 749.073 Da / Num. of mol.: 8 / Formula: C41H83NO8P / Discrete optimized protein energy / Comment: DOPE (phospholipid) *YM
#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 10 / Formula: C27H46O / Cholesterol
#4: Chemical ChemComp-BWQ / ~{tert}-butyl 3-[(2~{S},5~{S},8~{S})-14-cyclopentyloxy-2-(2-methylpropyl)-4,7-bis(oxidanylidene)-3,6,17-triazatetracyclo[8.7.0.0^{3,8}.0^{11,16}]heptadeca-1(10),11,13,15-tetraen-5-yl]propanoate


Mass: 523.664 Da / Num. of mol.: 2 / Formula: C30H41N3O5

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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

ComponentName: ATP-binding cassette sub-family G member 2 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
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
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: 100 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameCategory
1Gautomatchparticle selection
4CTFFINDCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 2098186
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 402348 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0099795
ELECTRON MICROSCOPYf_angle_d1.47113254
ELECTRON MICROSCOPYf_dihedral_angle_d7.3975940
ELECTRON MICROSCOPYf_chiral_restr0.0891528
ELECTRON MICROSCOPYf_plane_restr0.0071576

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