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- EMDB-0190: Cryo-EM structure of the ABCG2 E211Q mutant bound to ATP and Magnesium -

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Basic information

Entry
Database: EMDB / ID: 0190
TitleCryo-EM structure of the ABCG2 E211Q mutant bound to ATP and Magnesium
Map data
Sampleinhibitor-bound ABCG2
  • A mutant (E211Q) of the ATP-binding cassette sub-family G member 2
  • ATP-binding cassette sub-family G member 2
  • (ligand) x 2
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
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.09 Å resolution
AuthorsManolaridis I / Jackson SM / Taylor NMI / Kowal J / Stahlberg H / Locher KP
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 SM / Taylor NMI / Kowal J / Stahlberg H / Locher KP
Validation ReportPDB-ID: 6hbu

SummaryFull report
PDB-ID: 6hzm

SummaryFull report
About validation report
DateDeposition: Aug 13, 2018 / Header (metadata) release: Nov 7, 2018 / Map release: Nov 7, 2018 / Last update: Nov 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6hbu
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6hzm
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0190.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
0.81 Å/pix.
= 207.36 Å
256 pix
0.81 Å/pix.
= 207.36 Å
256 pix
0.81 Å/pix.
= 207.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density
Contour Level:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum-0.27293262 - 0.42899606
Average (Standard dev.)0.0010245538 (0.010962626)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 207.36 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z207.360207.360207.360
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2730.4290.001

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Supplemental data

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Sample components

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Entire inhibitor-bound ABCG2

EntireName: inhibitor-bound ABCG2 / Number of components: 5

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Component #1: protein, inhibitor-bound ABCG2

ProteinName: inhibitor-bound ABCG2 / Recombinant expression: No

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Component #2: protein, A mutant (E211Q) of the ATP-binding cassette sub-family ...

ProteinName: A mutant (E211Q) of the ATP-binding cassette sub-family G member 2
Recombinant expression: No
SourceSpecies: HOMO SAPIENS (human)
Source (engineered)Expression System: HOMO SAPIENS (human)

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Component #3: protein, ATP-binding cassette sub-family G member 2

ProteinName: ATP-binding cassette sub-family G member 2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 72.384867 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #5: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.4 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 165000.0 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4905

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 288447
3D reconstructionSoftware: RELION / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Overall bvalue: 136
Output model

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