[English] 日本語
Yorodumi
- PDB-5uj9: Cryo-EM structure of bovine multidrug resistance protein 1 (MRP1) -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5uj9
TitleCryo-EM structure of bovine multidrug resistance protein 1 (MRP1)
Descriptorbovine multidrug resistance protein 1 (MRP1),Multidrug resistance-associated protein 1
KeywordsTRANSPORT PROTEIN / ABC transporter / multidrug resistance
Specimen sourceBos taurus / mammal / Bovine / ウシ /
MethodElectron microscopy (3.49 A resolution / Single particle)
AuthorsJohnson, Z.L. / Chen, J.
CitationCell, 2017, 168, 1075-1085.e9

Cell, 2017, 168, 1075-1085.e9 StrPapers
Structural Basis of Substrate Recognition by the Multidrug Resistance Protein MRP1.
Zachary Lee Johnson / Jue Chen

DateDeposition: Jan 17, 2017 / Release: Feb 22, 2017 / Last modification: Mar 29, 2017

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8559
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: bovine multidrug resistance protein 1 (MRP1),Multidrug resistance-associated protein 1


Theoretical massNumber of molelcules
Total (without water)159,7021
Polyers159,7021
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

#1: Polypeptide(L)bovine multidrug resistance protein 1 (MRP1),Multidrug resistance-associated protein 1 / ATP-binding cassette sub-family C member 1 / Leukotriene C(4) transporter / LTC4 transporter


Mass: 159701.922 Da / Num. of mol.: 1 / Source: (gene. exp.) Bos taurus / mammal / ウシ / / References: UniProt: Q8HXQ5
Sequence detailsResidues 31-194, corresponding to TMD0, are modeled as poly-alanine. The register in this region could not be confidently established and thus the numbering assigned to the residues is putative. The poly-alanine regions have been renamed as unknown

+
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: bovine multidrug resistance protein 1 (MRP1) / Type: COMPLEX
Specimen supportGrid material: GOLD
Grid type: Quantifoil R1.2/1.3 400-mesh Au Holey Carbon Grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 37000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 80 K

-
Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
ComputingStructure refinement: REFMAC 5.8.0158
3D reconstructionResolution: 3.49 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 251986
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: RECIPROCAL
Refine

B iso mean: 265.842 A2 / Aniso B11: -6.2 A2 / Aniso B12: -0.4 A2 / Aniso B13: 2.19 A2 / Aniso B22: 4.38 A2 / Aniso B23: 0.61 A2 / Aniso B33: 1.82 A2 / Correlation coeff Fo to Fc: 0.969 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / R factor R work: 0.28564 / R factor obs: 0.28564 / Highest resolution: 3.49 A / Lowest resolution: 148 A / Number reflection obs: 88282 / Percent reflection obs: 99.99 / Overall ESU R: 0.448 / Solvent ion probe radii: 0.8 A / Solvent shrinkage radii: 0.8 A / Solvent vdw probe radii: 1.2 A / Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES / Solvent model details: MASK

Refine id
1
ELECTRON MICROSCOPY
Number of atoms included #1Total: 9857
Refine LS restraints
Refine idTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01910042
ELECTRON MICROSCOPYr_bond_other_d0.0000.0209686
ELECTRON MICROSCOPYr_angle_refined_deg1.0281.95713640
ELECTRON MICROSCOPYr_angle_other_deg3.7913.00022312
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.5485.0001286
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.40223.795390
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.13015.0001667
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.64115.00055
ELECTRON MICROSCOPYr_chiral_restr0.0540.2001619
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.02011130
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0202045
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it6.37427.3975171
ELECTRON MICROSCOPYr_mcbond_other6.37327.3955170
ELECTRON MICROSCOPYr_mcangle_it10.48941.0736448
ELECTRON MICROSCOPYr_mcangle_other10.48841.0756449
ELECTRON MICROSCOPYr_scbond_it6.42426.8854871
ELECTRON MICROSCOPYr_scbond_other6.42326.8794869
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other11.37440.2817192
ELECTRON MICROSCOPYr_long_range_B_refined17.84012003
ELECTRON MICROSCOPYr_long_range_B_other17.84012004
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.49 A / R factor R work: 0.765 / Lowest resolution: 3.581 A / Number reflection R free: 0 / Number reflection R work: 6547 / Total number of bins used: 20 / Percent reflection obs: 99.91

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more