[English] 日本語
Yorodumi
- EMDB-3425: Electron cryo-microscopy of human P-glycoprotein: ATP bound - clo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3425
TitleElectron cryo-microscopy of human P-glycoprotein: ATP bound - closed conformation
Map dataReconstruction of mutant (E556Q/E1201Q) human P-glycoprotein in an ATP binding state, bound to UIC2 Fab.
Sample
  • Sample: Human P-glycoprotein (E556Q/E1201Q) in ATP-binding, bound to UIC2 Fab
  • Protein or peptide: P-glycoprotein
  • Protein or peptide: UIC2 Fab
Keywordshuman P-Glycoprotein / ABCB1 / MDR-1 / closed conformation / ATP bound / UIC2 Fab
Function / homology
Function and homology information


positive regulation of anion channel activity / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / terpenoid transport / ceramide floppase activity / regulation of response to osmotic stress / floppase activity / ceramide translocation / Abacavir transmembrane transport / external side of apical plasma membrane ...positive regulation of anion channel activity / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / terpenoid transport / ceramide floppase activity / regulation of response to osmotic stress / floppase activity / ceramide translocation / Abacavir transmembrane transport / external side of apical plasma membrane / Atorvastatin ADME / phosphatidylethanolamine flippase activity / xenobiotic transport across blood-brain barrier / transepithelial transport / phosphatidylcholine floppase activity / xenobiotic detoxification by transmembrane export across the plasma membrane / export across plasma membrane / ABC-type xenobiotic transporter / P-type phospholipid transporter / ABC-type xenobiotic transporter activity / phospholipid translocation / Prednisone ADME / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / transport across blood-brain barrier / xenobiotic metabolic process / regulation of chloride transport / stem cell proliferation / ABC-family proteins mediated transport / transmembrane transport / G2/M transition of mitotic cell cycle / response to xenobiotic stimulus / apical plasma membrane / ubiquitin protein ligase binding / cell surface / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporter-like, conserved site / ABC transporters family signature. / 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
ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.0 Å
AuthorsFrank GA / Shukla S / Rao P / Borgnia MJ / Bartesaghi A / Merk A / Mobin A / Esser L / Earl LA / Gottesman MM ...Frank GA / Shukla S / Rao P / Borgnia MJ / Bartesaghi A / Merk A / Mobin A / Esser L / Earl LA / Gottesman MM / Xia D / Ambudkar SV / Subramaniam S
CitationJournal: Mol Pharmacol / Year: 2016
Title: Cryo-EM Analysis of the Conformational Landscape of Human P-glycoprotein (ABCB1) During its Catalytic Cycle.
Authors: Gabriel A Frank / Suneet Shukla / Prashant Rao / Mario J Borgnia / Alberto Bartesaghi / Alan Merk / Aerfa Mobin / Lothar Esser / Lesley A Earl / Michael M Gottesman / Di Xia / Suresh V ...Authors: Gabriel A Frank / Suneet Shukla / Prashant Rao / Mario J Borgnia / Alberto Bartesaghi / Alan Merk / Aerfa Mobin / Lothar Esser / Lesley A Earl / Michael M Gottesman / Di Xia / Suresh V Ambudkar / Sriram Subramaniam /
Abstract: The multidrug transporter P-glycoprotein (P-gp, ABCB1) is an ATP-dependent pump that mediates the efflux of structurally diverse drugs and xenobiotics across cell membranes, affecting drug ...The multidrug transporter P-glycoprotein (P-gp, ABCB1) is an ATP-dependent pump that mediates the efflux of structurally diverse drugs and xenobiotics across cell membranes, affecting drug pharmacokinetics and contributing to the development of multidrug resistance. Structural information about the conformational changes in human P-gp during the ATP hydrolysis cycle has not been directly demonstrated, although mechanistic information has been inferred from biochemical and biophysical studies conducted with P-gp and its orthologs, or from structures of other ATP-binding cassette transporters. Using single-particle cryo-electron microscopy, we report the surprising discovery that, in the absence of the transport substrate and nucleotides, human P-gp can exist in both open [nucleotide binding domains (NBDs) apart; inward-facing] and closed (NBDs close; outward-facing) conformations. We also probe conformational states of human P-gp during the catalytic cycle, and demonstrate that, following ATP hydrolysis, P-gp transitions through a complete closed conformation to a complete open conformation in the presence of ADP.
History
DepositionMay 8, 2016-
Header (metadata) releaseJun 15, 2016-
Map releaseJun 22, 2016-
UpdateJun 22, 2016-
Current statusJun 22, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3425.png

Downloads & links

-
Map

FileDownload / File: emd_3425.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of mutant (E556Q/E1201Q) human P-glycoprotein in an ATP binding state, bound to UIC2 Fab.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 224 pix.
= 314.272 Å		1.4 Å/pix.
x 224 pix.
= 314.272 Å		1.4 Å/pix.
x 224 pix.
= 314.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.403 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.01159302 - 0.09791175
Average (Standard dev.)0.00111353 (±0.00856277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 314.272 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4031.4031.403
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z314.272314.272314.272
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0120.0980.001

-
Supplemental data

-
Sample components

-
Entire : Human P-glycoprotein (E556Q/E1201Q) in ATP-binding, bound to UIC2 Fab

EntireName: Human P-glycoprotein (E556Q/E1201Q) in ATP-binding, bound to UIC2 Fab
Components
  • Sample: Human P-glycoprotein (E556Q/E1201Q) in ATP-binding, bound to UIC2 Fab
  • Protein or peptide: P-glycoprotein
  • Protein or peptide: UIC2 Fab

-
Supramolecule #1000: Human P-glycoprotein (E556Q/E1201Q) in ATP-binding, bound to UIC2 Fab

SupramoleculeName: Human P-glycoprotein (E556Q/E1201Q) in ATP-binding, bound to UIC2 Fab
type: sample / ID: 1000
Oligomeric state: One monomer of P-glycoprotein bound to one UIC2 Fab
Number unique components: 2
Molecular weightTheoretical: 190 KDa

-
Macromolecule #1: P-glycoprotein

MacromoleculeName: P-glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: P-gp, Pgp, ABCB1, MDR1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane
Molecular weightTheoretical: 141 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant strain: BTI-TN-5B1-4 / Recombinant cell: High Five insect cells
SequenceUniProtKB: ATP-dependent translocase ABCB1
InterPro: AAA+ ATPase domain, ABC transporter type 1, transmembrane domain, ABC transporter-like, ATP-binding domain, ABC transporter-like, conserved site, P-loop containing nucleoside triphosphate hydrolase

-
Macromolecule #2: UIC2 Fab

MacromoleculeName: UIC2 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: mouse / Tissue: Spleen / Cell: B cells
Molecular weightTheoretical: 50 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Hybridoma

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Details: 10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.09% n-Dodecyl Betta-D-maltoside
GridDetails: 200 mesh Cu R1.2/1.3 holey carbon grids from Quantifoil, plasma-cleaned
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 83 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Cs0
DateNov 19, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 2027 / Average electron dose: 30 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 47000 / Cs: mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Detailshe particles were selected using an automatic selection program.
CTF correctionDetails: CTF parameters obtained from whole micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: OTHER / Software - Name: EMAN2, Relion, 1.3 / Number images used: 14158
Final two d classificationNumber classes: 5

-
Atomic model buiding 1

Initial modelPDB ID:

4m1m

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Overlap

-
Atomic model buiding 2

Initial modelPDB ID:

4ksc

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Overlap

-
Atomic model buiding 3

Initial modelPDB ID:

2hyd

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Overlap

-
Atomic model buiding 4

Initial modelPDB ID:

4pl0

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Overlap

+
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