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- EMDB-45099: Leukotriene C4-bound Multidrug Resistance-associated Protein 2 (MRP2) -

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Basic information

Entry
Database: EMDB / ID: EMD-45099
TitleLeukotriene C4-bound Multidrug Resistance-associated Protein 2 (MRP2)
Map dataLTC4-bound MRP2 map
Sample
  • Cell: wild type MRP2 bound to its substrate, leukotriene C4
    • Protein or peptide: ATP-binding cassette sub-family C member 2
  • Ligand: (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-3-( 2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid
  • Ligand: CHOLESTEROL
  • Ligand: UNKNOWN LIGAND
KeywordsABC transporter / Multidrug resistance / Substrate / TRANSPORT 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 / ABC-type glutathione S-conjugate transporter activity / ATPase-coupled inorganic anion transmembrane transporter activity / Atorvastatin ADME / xenobiotic transmembrane transport ...Defective ABCC2 causes DJS / bilirubin transmembrane transporter activity / bilirubin transport / xenobiotic export from cell / leukotriene transport / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / ATPase-coupled inorganic anion transmembrane transporter activity / Atorvastatin ADME / xenobiotic transmembrane transport / heme catabolic process / xenobiotic transport across blood-brain barrier / organic anion transmembrane transporter activity / transepithelial transport / intercellular canaliculus / 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 / bile acid and bile salt transport / Heme degradation / 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 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 ...Multi drug resistance-associated protein / : / 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: 2.75 Å
AuthorsKoide E / Chen J
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 28, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45099.png

Downloads & links

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Map

FileDownload / File: emd_45099.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLTC4-bound MRP2 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 480 pix.
= 356.64 Å		0.74 Å/pix.
x 480 pix.
= 356.64 Å		0.74 Å/pix.
x 480 pix.
= 356.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.62752575 - 1.143261
Average (Standard dev.)0.00015099667 (±0.021149907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 356.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45099_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_45099_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_45099_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : wild type MRP2 bound to its substrate, leukotriene C4

EntireName: wild type MRP2 bound to its substrate, leukotriene C4
Components
  • Cell: wild type MRP2 bound to its substrate, leukotriene C4
    • Protein or peptide: ATP-binding cassette sub-family C member 2
  • Ligand: (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-3-( 2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid
  • Ligand: CHOLESTEROL
  • Ligand: UNKNOWN LIGAND

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Supramolecule #1: wild type MRP2 bound to its substrate, leukotriene C4

SupramoleculeName: wild type MRP2 bound to its substrate, leukotriene C4 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 174.392344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLEKFCNSTF WNSSFLDSPE ADLPLCFEQT VLVWIPLGYL WLLAPWQLLH VYKSRTKRSS TTKLYLAKQV FVGFLLILAA IELALVLTE DSGQATVPAV RYTNPSLYLG TWLLVLLIQY SRQWCVQKNS WFLSLFWILS ILCGTFQFQT LIRTLLQGDN S NLAYSCLF ...String:
MLEKFCNSTF WNSSFLDSPE ADLPLCFEQT VLVWIPLGYL 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 STKF

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

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Macromolecule #2: (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-[[(4~{S})-4-...

MacromoleculeName: (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-3-( 2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl- ...Name: (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-3-( 2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: LTX
Molecular weightTheoretical: 625.774 Da

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 5 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 4 / Number of copies: 13 / Formula: UNL
Molecular weightTheoretical: 790.145 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.06 %DigitoninDigitonin
150.0 mMNaClsodium chloride
50.0 mMTrisTris
2.0 mMMgCl2magnesium chloride
2.0 mMDTTDTT

Details: Digitonin is solubilized overnight. prior to use, it is filtered using a 0.22 uM filter.
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Detailssingle-particle MRP2 in digitonin micelle. Mixed with 285 uM LTC4.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83725
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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