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- EMDB-0196: Cryo-EM structure of the ABCG2 E211Q mutant bound to estrone 3-su... -

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Basic information

Entry
Database: EMDB / ID: 0196
TitleCryo-EM structure of the ABCG2 E211Q mutant bound to estrone 3-sulfate and 5D3-Fab
Map dataABCG2 in complex with estrone-3-sulfate and 5D3-Fab
Samplenanodisc-reconsituted ABCG2 E211Q mutant bound to estrone 3-sulfate and 5D3-Fab
  • ABCG2 E211Q mutant
  • 5D3-Fab
  • ATP-binding cassette sub-family G member 2
  • 5D3-Fab light chain
  • 5D3-Fab heavy chain
  • (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) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 3.58 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: 6hco

SummaryFull reportAbout validation report
DateDeposition: Aug 15, 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: 0.32
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.32
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6hco
  • Surface level: 0.32
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0196.map.gz (map file in CCP4 format, 219489 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
380 pix
0.81 Å/pix.
= 308.56 Å
380 pix
0.81 Å/pix.
= 308.56 Å
380 pix
0.81 Å/pix.
= 308.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.812 Å
Density
Contour Level:0.32 (by author), 0.32 (movie #1):
Minimum - Maximum-0.3993025 - 1.1154133
Average (Standard dev.)0.0039930413 (0.040745053)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions380380380
Origin0.00.00.0
Limit379.0379.0379.0
Spacing380380380
CellA=B=C: 308.56 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8120.8120.812
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z308.560308.560308.560
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.3991.1150.004

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Supplemental data

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Sample components

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Entire nanodisc-reconsituted ABCG2 E211Q mutant bound to estrone 3-sulfa...

EntireName: nanodisc-reconsituted ABCG2 E211Q mutant bound to estrone 3-sulfate and 5D3-Fab
Number of components: 8

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Component #1: protein, nanodisc-reconsituted ABCG2 E211Q mutant bound to estron...

ProteinName: nanodisc-reconsituted ABCG2 E211Q mutant bound to estrone 3-sulfate and 5D3-Fab
Recombinant expression: No

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Component #2: protein, ABCG2 E211Q mutant

ProteinName: ABCG2 E211Q mutant / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293 EBNA

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Component #3: protein, 5D3-Fab

ProteinName: 5D3-Fab / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #4: 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: 73.394758 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, 5D3-Fab light chain

ProteinName: 5D3-Fab light chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.594016 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #6: protein, 5D3-Fab heavy chain

ProteinName: 5D3-Fab heavy chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.843633 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #7: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #8: ligand, estrone 3-sulfate

LigandName: estrone 3-sulfate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.350429 kDa

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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: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3984

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 42790
3D reconstructionSoftware: cryoSPARC / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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