[English] 日本語
Yorodumi
- EMDB-2715: Electron cryo-microscopy of ABCG2 from two-dimensional crystals -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2715
TitleElectron cryo-microscopy of ABCG2 from two-dimensional crystals
Map dataNon-crystallographic symmetry averaging around the local C2 symmetry axis was applied to the raw ABCG2 map.
Sample
  • Sample: ABCG2 (breast cancer resistance protein).
  • Protein or peptide: ATP-binding cassette sub-family G member 2
KeywordsABCG2 / BCRP / Cryo-EM / 3D structure / ABC transporter
Function / homology
Function and homology information


transport / small molecule metabolic process / biotin transmembrane transporter activity / biotin transport / heme transport / riboflavin transport / riboflavin transmembrane transporter activity / renal urate salt excretion / urate transmembrane transporter activity / urate metabolic process ...transport / small molecule metabolic process / biotin transmembrane transporter activity / biotin transport / heme transport / riboflavin transport / riboflavin transmembrane transporter activity / renal urate salt excretion / urate transmembrane transporter activity / urate metabolic process / response to xenobiotic stimulus => GO:0009410 / Abacavir transmembrane transport / external side of apical plasma membrane / organic anion transport / xenobiotic transmembrane transport / organic anion transmembrane transporter activity / xenobiotic transport across blood-brain barrier / export across plasma membrane / ABC-type xenobiotic transporter / Paracetamol ADME / Ciprofloxacin ADME / transepithelial transport / ABC-type xenobiotic transporter activity / cellular detoxification / NFE2L2 regulating MDR associated enzymes / xenobiotic transport / Heme biosynthesis / Heme degradation / lipid transport / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transport across blood-brain barrier / ATPase-coupled transmembrane transporter activity / mitochondrial membrane / brush border membrane / Iron uptake and transport / transmembrane transport / intracellular iron ion homeostasis / apical plasma membrane / membrane raft / ATP hydrolysis activity / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
ABC transporter family G domain / ABC-2 type transporter / ABC-2 type transporter / ABC-2 type transporter / ABC-2 type transporter / ABC transporter / ABC transporter-like, ATP-binding domain / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities ...ABC transporter family G domain / ABC-2 type transporter / ABC-2 type transporter / ABC-2 type transporter / ABC-2 type transporter / ABC transporter / ABC transporter-like, ATP-binding domain / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Broad substrate specificity ATP-binding cassette transporter ABCG2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodelectron crystallography / cryo EM / negative staining / Resolution: 18.0 Å
AuthorsRosenberg MF / Bikadi Z / Hazai E / Starborg T / Kelley L / Chayen NE / Ford RC / Mao Q
CitationJournal: Acta Crystallogr D Biol Crystallogr / Year: 2015
Title: Three-dimensional structure of the human breast cancer resistance protein (BCRP/ABCG2) in an inward-facing conformation.
Authors: Mark F Rosenberg / Zsolt Bikadi / Eszter Hazai / Tobias Starborg / Lawrence Kelley / Naomi E Chayen / Robert C Ford / Qingcheng Mao /
Abstract: ABCG2 is an efflux drug transporter that plays an important role in drug resistance and drug disposition. In this study, the first three-dimensional structure of human full-length ABCG2 analysed by ...ABCG2 is an efflux drug transporter that plays an important role in drug resistance and drug disposition. In this study, the first three-dimensional structure of human full-length ABCG2 analysed by electron crystallography from two-dimensional crystals in the absence of nucleotides and transported substrates is reported at 2 nm resolution. In this state, ABCG2 forms a symmetric homodimer with a noncrystallographic twofold axis perpendicular to the two-dimensional crystal plane, as confirmed by subtomogram averaging. This configuration suggests an inward-facing configuration similar to murine ABCB1, with the nucleotide-binding domains (NBDs) widely separated from each other. In the three-dimensional map, densities representing the long cytoplasmic extensions from the transmembrane domains that connect the NBDs are clearly visible. The structural data have allowed the atomic model of ABCG2 to be refined, in which the two arms of the V-shaped ABCG2 homodimeric complex are in a more closed and narrower conformation. The structural data and the refined model of ABCG2 are compatible with the biochemical analysis of the previously published mutagenesis studies, providing novel insight into the structure and function of the transporter.
History
DepositionJul 23, 2014-
Header (metadata) releaseAug 6, 2014-
Map releaseJul 15, 2015-
UpdateAug 19, 2015-
Current statusAug 19, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2715.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-crystallographic symmetry averaging around the local C2 symmetry axis was applied to the raw ABCG2 map.
Voxel sizeX: 3.2 Å / Y: 3.2 Å / Z: 3.3 Å
Density
Contour LevelBy AUTHOR: 1.8 / Movie #1: 1.8
Minimum - Maximum-7.10321522 - 13.60273933
Average (Standard dev.)0.01877212 (±0.38814983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-37-4717
Dimensions7211788
Spacing7211788
CellA: 374.4 Å / B: 230.40001 Å / C: 290.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.23.23.3
M x/y/z1177288
origin x/y/z0.0000.0000.000
length x/y/z374.400230.400290.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-47-3717
NC/NR/NS1177288
D min/max/mean-7.10313.6030.019

-
Supplemental data

-
Sample components

-
Entire : ABCG2 (breast cancer resistance protein).

EntireName: ABCG2 (breast cancer resistance protein).
Components
  • Sample: ABCG2 (breast cancer resistance protein).
  • Protein or peptide: ATP-binding cassette sub-family G member 2

-
Supramolecule #1000: ABCG2 (breast cancer resistance protein).

SupramoleculeName: ABCG2 (breast cancer resistance protein). / type: sample / ID: 1000 / Details: Two-dimensional crystals of purified ABCG2. / Oligomeric state: Homodimer / Number unique components: 1
Molecular weightExperimental: 70 KDa / Theoretical: 70 KDa / Method: SDS-PAGE.

-
Macromolecule #1: ATP-binding cassette sub-family G member 2

MacromoleculeName: ATP-binding cassette sub-family G member 2 / type: protein_or_peptide / ID: 1 / Name.synonym: Breast cancer resistance protein
Details: Purified ABCG2 formed two-dimensional crystals on a carbon electron microscopy grid.
Number of copies: 2 / Oligomeric state: Homodimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane
Molecular weightExperimental: 70 KDa / Theoretical: 70 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus) / Recombinant strain: KM71 / Recombinant plasmid: pHIL-BCRP-His10
SequenceUniProtKB: Broad substrate specificity ATP-binding cassette transporter ABCG2
GO: intracellular iron ion homeostasis, xenobiotic transmembrane transport, heme transport, response to xenobiotic stimulus => GO:0009410, small molecule metabolic process, transmembrane transport, ...GO: intracellular iron ion homeostasis, xenobiotic transmembrane transport, heme transport, response to xenobiotic stimulus => GO:0009410, small molecule metabolic process, transmembrane transport, transport, urate metabolic process, xenobiotic transport
InterPro: AAA+ ATPase domain, ABC-2 type transporter, ABC transporter-like, ATP-binding domain, P-loop containing nucleoside triphosphate hydrolase

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingelectron crystallography
Aggregation state2D array

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 8
Details: 50 mM Tris-HCl , 10% glycerol, 1 mM 2-mercaptoethanol, and 0.187 mg/ml DDM.
StainingType: NEGATIVE
Details: Some grids were negatively stained with 2 % w/v uranyl-acetate for 60 seconds.
GridDetails: 300 mesh gold/carbon grids with thick carbon support (5-10 nm) .
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 98 K / Instrument: FEI VITROBOT MARK III
Method: 2-D crystals growing epitaxially on the grid surface were blotted for 1 second before plunging.
DetailsCrystals were grown epitaxially on the surface of carbon grids.
Crystal formationDetails: Crystals were grown epitaxially on the surface of carbon grids.

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 79730 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.02 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Liquid nitrogen cooled. Standard Polara cartridge.
Specimen holder model: OTHER / Tilt angle max: 60 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 60 °
TemperatureMin: 80 K / Max: 105 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 130,000 times magnification.
DateOct 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 76 / Average electron dose: 12 e/Å2 / Bits/pixel: 16
Tilt angle min0
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Crystal parametersUnit cell - A: 70 Å / Unit cell - B: 123 Å / Unit cell - C: 200 Å / Unit cell - γ: 90 ° / Unit cell - α: 90.0 ° / Unit cell - β: 90.0 ° / Plane group: P 1 21
CTF correctionDetails: Algorithm in 2dx.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: OTHER / Software - Name: 2dx / Details: Final maps were calculated with CCP4.
DetailsImages were unbent using 2dx.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more