[English] 日本語
Yorodumi
- EMDB-35868: Multidrug resistance-associated protein 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35868
TitleMultidrug resistance-associated protein 3
Map dataMRP2 includes 1 NBD
Sample
  • Complex: multidrug resistance-associated protein 3 in apo state
    • Protein or peptide: ATP-binding cassette sub-family C member 2
KeywordsATP-binding cassette transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective ABCC2 causes DJS / bilirubin transmembrane transporter activity / bilirubin transport / xenobiotic export from cell / leukotriene transport / ABC-type glutathione S-conjugate transporter activity / ABC-type glutathione-S-conjugate transporter / : / heme catabolic process / Atorvastatin ADME ...Defective ABCC2 causes DJS / bilirubin transmembrane transporter activity / bilirubin transport / xenobiotic export from cell / leukotriene transport / ABC-type glutathione S-conjugate transporter activity / ABC-type glutathione-S-conjugate transporter / : / heme catabolic process / Atorvastatin ADME / xenobiotic transport across blood-brain barrier / xenobiotic transmembrane transport / intercellular canaliculus / : / transepithelial transport / Paracetamol ADME / ABC-type xenobiotic transporter / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity / Heme degradation / bile acid and bile salt transport / Aspirin ADME / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transport across blood-brain barrier / xenobiotic metabolic process / ABC-family proteins mediated transport / transmembrane transport / apical plasma membrane / negative regulation of gene expression / cell surface / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Multi drug resistance-associated protein / : / ABC transporter TMD0 domain / : / ABC transporter transmembrane region / 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 transporters family signature. ...Multi drug resistance-associated protein / : / ABC transporter TMD0 domain / : / ABC transporter transmembrane region / 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 transporters family signature. / ABC transporter / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-binding cassette sub-family C member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsYun CH / Gao HM
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: structure of multidrug resistance-associated protein 2 at 3.62 Angstroms resolution
Authors: Yun CH / Gao HM
History
DepositionApr 7, 2023-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_35868.png

Downloads & links

-
Map

FileDownload / File: emd_35868.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMRP2 includes 1 NBD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.119
Minimum - Maximum-0.6272317 - 0.74504817
Average (Standard dev.)-0.00019847538 (±0.017590621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map

Fileemd_35868_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map

Fileemd_35868_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : multidrug resistance-associated protein 3 in apo state

EntireName: multidrug resistance-associated protein 3 in apo state
Components
  • Complex: multidrug resistance-associated protein 3 in apo state
    • Protein or peptide: ATP-binding cassette sub-family C member 2

-
Supramolecule #1: multidrug resistance-associated protein 3 in apo state

SupramoleculeName: multidrug resistance-associated protein 3 in apo state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: ATP-binding cassette sub-family C member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 179.447438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLEKFCNSTF WNSSFLDSPE ADLPLCFEQT VLVWIPLGFL WLLAPWQLLH VYKSRTKRSS TTKLYLAKQV FVGFLLILAA IELALVLTE DSGQATVPAV RYTNPSLYLG TWLLVLLIQY SRQWCVQKNS WFLSLFWILS ILCGTFQFQT LIRTLLQGDN S NLAYSCLF ...String:
MLEKFCNSTF WNSSFLDSPE ADLPLCFEQT VLVWIPLGFL WLLAPWQLLH VYKSRTKRSS TTKLYLAKQV FVGFLLILAA IELALVLTE DSGQATVPAV RYTNPSLYLG TWLLVLLIQY SRQWCVQKNS WFLSLFWILS ILCGTFQFQT LIRTLLQGDN S NLAYSCLF FISYGFQILI LIFSAFSENN ESSNNPSSIA SFLSSITYSW YDSIILKGYK RPLTLEDVWE VDEEMKTKTL VS KFETHMK RELQKARRAL QRRQEKSSQQ NSGARLPGLN KNQSQSQDAL VLEDVEKKKK KSGTKKDVPK SWLMKALFKT FYM VLLKSF LLKLVNDIFT FVSPQLLKLL ISFASDRDTY LWIGYLCAIL LFTAALIQSF CLQCYFQLCF KLGVKVRTAI MASV YKKAL TLSNLARKEY TVGETVNLMS VDAQKLMDVT NFMHMLWSSV LQIVLSIFFL WRELGPSVLA GVGVMVLVIP INAIL STKS KTIQVKNMKN KDKRLKIMNE ILSGIKILKY FAWEPSFRDQ VQNLRKKELK NLLAFSQLQC VVIFVFQLTP VLVSVV TFS VYVLVDSNNI LDAQKAFTSI TLFNILRFPL SMLPMMISSM LQASVSTERL EKYLGGDDLD TSAIRHDCNF DKAMQFS EA SFTWEHDSEA TVRDVNLDIM AGQLVAVIGP VGSGKSSLIS AMLGEMENVH GHITIKGTTA YVPQQSWIQN GTIKDNIL F GTEFNEKRYQ QVLEACALLP DLEMLPGGDL AEIGEKGINL SGGQKQRISL ARATYQNLDI YLLDDPLSAV DAHVGKHIF NKVLGPNGLL KGKTRLLVTH SMHFLPQVDE IVVLGNGTIV EKGSYSALLA KKGEFAKNLK TFLRHTGPEE EATVHDGSEE EDDDYGLIS SVEEIPEDAA SITMRRENSF RRTLSRSSRS NGRHLKSLRN SLKTRNVNSL KEDEELVKGQ KLIKKEFIET G KVKFSIYL EYLQAIGLFS IFFIILAFVM NSVAFIGSNL WLSAWTSDSK IFNSTDYPAS QRDMRVGVYG ALGLAQGIFV FI AHFWSAF GFVHASNILH KQLLNNILRA PMRFFDTTPT GRIVNRFAGD ISTVDDTLPQ SLRSWITCFL GIISTLVMIC MAT PVFTII VIPLGIIYVS VQMFYVSTSR QLRRLDSVTR SPIYSHFSET VSGLPVIRAF EHQQRFLKHN EVRIDTNQKC VFSW ITSNR WLAIRLELVG NLTVFFSALM MVIYRDTLSG DTVGFVLSNA LNITQTLNWL VRMTSEIETN IVAVERITEY TKVEN EAPW VTDKRPPPDW PSKGKIQFNN YQVRYRPELD LVLRGITCDI GSMEKIGVVG RTGAGKSSLT NCLFRILEAA GGQIII DGV DIASIGLHDL REKLTIIPQD PILFSGSLRM NLDPFNNYSD EEIWKALELA HLKSFVASLQ LGLSHEVTEA GGNLSIG QR QLLCLGRALL RKSKILVLDE ATAAVDLETD NLIQTTIQNE FAHCTVITIA HRLHTIMDSD KVMVLDNGKI IECGSPEE L LQIPGPFYFM AKEAGIENVN STKFLEENLY FQGSGGGGGG DYKDHDGDYK DHDIDYKDDD DKHHHHHH

UniProtKB: ATP-binding cassette sub-family C member 2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.00 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124494
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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