[English] 日本語
Yorodumi
- PDB-6ujr: P-glycoprotein mutant-F724A and C952A-with BDE100 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ujr
TitleP-glycoprotein mutant-F724A and C952A-with BDE100
ComponentsATP-dependent translocase ABCB1
KeywordsTRANSLOCASE / P-glycoprotein / MDR1 / P-gp / Pgp / Multidrug Resistance Protein
Function / homology
Function and homology information


hormone transport / cellular response to nonylphenol / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / negative regulation of sensory perception of pain ...hormone transport / cellular response to nonylphenol / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / negative regulation of sensory perception of pain / positive regulation of establishment of Sertoli cell barrier / regulation of intestinal absorption / response to quercetin / cellular response to external biotic stimulus / response to antineoplastic agent / Prednisone ADME / terpenoid transport / ceramide floppase activity / establishment of blood-retinal barrier / response to glycoside / protein localization to bicellular tight junction / ceramide translocation / floppase activity / ABC-family proteins mediated transport / response to thyroxine / establishment of blood-brain barrier / phosphatidylethanolamine flippase activity / phosphatidylcholine floppase activity / cellular response to L-glutamate / xenobiotic transport across blood-brain barrier / intercellular canaliculus / xenobiotic detoxification by transmembrane export across the plasma membrane / response to vitamin D / export across plasma membrane / P-type phospholipid transporter / ABC-type xenobiotic transporter / response to alcohol / response to vitamin A / response to glucagon / intestinal absorption / ABC-type xenobiotic transporter activity / cellular response to antibiotic / phospholipid translocation / cellular hyperosmotic salinity response / cellular response to alkaloid / maintenance of blood-brain barrier / efflux transmembrane transporter activity / transmembrane transporter activity / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / response to progesterone / female pregnancy / placenta development / cellular response to estradiol stimulus / brush border membrane / circadian rhythm / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / apical plasma membrane / response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Type 1 protein exporter / 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. ...Type 1 protein exporter / 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
2,4-dibromophenyl 2,4,6-tribromophenyl ether / ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsAller, S.G. / Le, C.A.
CitationJournal: Iucrj / Year: 2020
Title: Structural definition of polyspecific compensatory ligand recognition by P-glycoprotein.
Authors: Le, C.A. / Harvey, D.S. / Aller, S.G.
History
DepositionOct 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent translocase ABCB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,1342
Polymers141,5701
Non-polymers5651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.397, 138.027, 193.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ATP-dependent translocase ABCB1 / ATP-binding cassette sub-family B member 1A / MDR1A / Multidrug resistance protein 1A / Multidrug ...ATP-binding cassette sub-family B member 1A / MDR1A / Multidrug resistance protein 1A / Multidrug resistance protein 3 / P-glycoprotein 3 / Phospholipid transporter ABCB1


Mass: 141569.531 Da / Num. of mol.: 1 / Mutation: N83Q,N87Q, N90Q,F724A, C952A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abcb1a, Abcb4, Mdr1a, Mdr3, Pgy-3, Pgy3 / Production host: Komagataella pastoris (fungus)
References: UniProt: P21447, ABC-type xenobiotic transporter, P-type phospholipid transporter
#2: Chemical ChemComp-4C8 / 2,4-dibromophenyl 2,4,6-tribromophenyl ether


Mass: 564.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H5Br5O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.37 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: Hepes, lithium sulfate, EDTA, polyethylene glycol (PEG) 600 (pH 7.9 to 8.4)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91963 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91963 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. obs: 36639 / % possible obs: 85.2 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Χ2: 0.541 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.1-4.492.70.813280.710.4750.9520.3693.2
4.49-4.5811.50.5318260.90.1610.5560.44496.7
4.58-4.6812.90.4888460.9410.140.5080.43199.8
4.68-4.7912.60.4338630.9590.1250.4510.43299.8
4.79-4.9112.50.3538520.9640.1030.3680.429100
4.91-5.0413.70.3478840.9730.0960.360.42599.8
5.04-5.1913.80.3088530.9790.0850.320.4499.8
5.19-5.3513.70.2848650.9840.0790.2950.43499.9
5.35-5.5413.70.2668660.9840.0740.2770.44399.9
5.54-5.7713.60.2418620.9870.0670.2510.4499.9
5.77-6.0313.30.2118810.9920.0590.2190.44799.9
6.03-6.35130.1598670.9930.0460.1660.45199.9
6.35-6.74120.138750.9950.0390.1360.46399.9
6.74-7.2612.60.0998770.9980.0290.1030.47399.9
7.26-7.9912.90.0718880.9980.020.0740.48299.9
7.99-9.1413.40.0559080.9980.0160.0580.547100
9.14-11.4912.60.0499080.9990.0140.0510.634100
11.49-5011.70.0469800.9990.0140.0481.7899.8

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHENIX1.14-3260-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xwk without BDE100

4xwk


Resolution: 4.1→29.81 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.57
RfactorNum. reflection% reflection
Rfree0.2946 3479 9.5 %
Rwork0.2714 --
obs0.2735 36639 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 343.22 Å2 / Biso mean: 217.5254 Å2 / Biso min: 137.22 Å2
Refinement stepCycle: final / Resolution: 4.1→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9157 0 18 0 9175
Biso mean--238.37 --
Num. residues----1182
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.1-4.160.36651340.35113111445100
4.16-4.220.30271360.327413261462100
4.22-4.280.3421430.309113471490100
4.28-4.340.33331400.300113251465100
4.34-4.420.33021300.309412911421100
4.42-4.490.30541420.300713531495100
4.49-4.570.34161430.296913271470100
4.57-4.660.2641380.280113381476100
4.66-4.760.29911410.293513541495100
4.76-4.860.32461380.264312981436100
4.86-4.970.34071380.284513421480100
4.97-5.090.28331380.284913181456100
5.09-5.230.29951370.285313051442100
5.23-5.380.32831420.29513401482100
5.38-5.560.27351440.301513321476100
5.56-5.750.31051420.30213101452100
5.75-5.980.37411400.302213391479100
5.98-6.250.32751340.293513211455100
6.25-6.580.31981440.312113211465100
6.58-6.990.28311370.294113351472100
6.99-7.520.32141390.263713361475100
7.52-8.260.29671390.251213211460100
8.26-9.420.23151370.213513261463100
9.42-11.740.21591440.205913211465100
11.76-29.810.33481390.30011323146299

+
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