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- EMDB-65283: Cryo-EM structure of Oryza sativa multidrug resistance protein 5 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-65283
TitleCryo-EM structure of Oryza sativa multidrug resistance protein 5 (MRP5)
Map data
Sample
  • Complex: Multidrug-resistance associated protein 5
    • Protein or peptide: ABC transporter C family member 13
KeywordsABC-type transporter / Monomer / TRANSPORT PROTEIN
Function / homology
Function and homology information


Translocases / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
ABC transporter C family, six-transmembrane helical domain 2 / ABC transporter C family, six-transmembrane helical domain 1 / : / 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 C family, six-transmembrane helical domain 2 / ABC transporter C family, six-transmembrane helical domain 1 / : / 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
ABC transporter C family member 13
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsZou J / Zhang J / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32422041 China
CitationJournal: Plant Cell / Year: 2026
Title: Cryo-EM structures of Oryza sativa MRP5 reveal a phytate accumulation mechanism in plant vacuoles.
Authors: Jiaqi Zuo / Jie Zhang / Ying Tang / Lihuan Jiang / Shuo Cao / Yan Liu / Cuicui Shen / Chuang Wang / Hao Chen / Lizhong Xiong / Ping Yin / Zhou Gong / Zhu Liu /
Abstract: Phytate (phytic acid, or InsP6), the primary phosphorus storage compound in plants, plays essential roles in nutrient homeostasis and cellular signaling. However, its strong metal-chelating ...Phytate (phytic acid, or InsP6), the primary phosphorus storage compound in plants, plays essential roles in nutrient homeostasis and cellular signaling. However, its strong metal-chelating properties make cytosolic accumulation cytotoxic, necessitating its sequestration into vacuoles for safe storage. Here, we present the cryo-EM structures of the rice vacuolar phytate transporter, OsMRP5, captured in distinct functional states. These structures reveal the molecular basis of OsMRP5 function as an ATP-binding cassette (ABC) transporter. OsMRP5 employs a specialized substrate-recognition mechanism, uniquely adapted to bind the fully hydrophilic InsP6 through extensive electrostatic and hydrogen-bonding interactions within two distinct, highly polar binding sites in its central cavity. A distinctive electropositive tunnel, positioned above the central cavity, forms a continuous pathway connecting the InsP6-binding pocket to the vacuolar export site. This tunnel likely generates an electrostatic attraction that facilitates the movement of the highly anionic InsP6 through the transporter. By mapping mutations from low-phytic acid (lpa) crop variants onto the OsMRP5 structures, we pinpoint their conserved locations critical for transporter function and validate their impact experimentally. These results reveal how OsMRP5 recognizes and transports the highly charged InsP6 molecule into vacuoles, providing a molecular framework for targeted manipulation of this agriculturally important transporter.
History
DepositionJul 6, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65283.png

Downloads & links

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Map

FileDownload / File: emd_65283.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 263.68 Å		0.82 Å/pix.
x 320 pix.
= 263.68 Å		0.82 Å/pix.
x 320 pix.
= 263.68 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-0.44013458 - 0.83899117
Average (Standard dev.)-0.000121073164 (±0.012977024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65283_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_65283_half_map_2.map
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Sample components

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Entire : Multidrug-resistance associated protein 5

EntireName: Multidrug-resistance associated protein 5
Components
  • Complex: Multidrug-resistance associated protein 5
    • Protein or peptide: ABC transporter C family member 13

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Supramolecule #1: Multidrug-resistance associated protein 5

SupramoleculeName: Multidrug-resistance associated protein 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

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Macromolecule #1: ABC transporter C family member 13

MacromoleculeName: ABC transporter C family member 13 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Translocases
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 166.321906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPHFPNLPLP EAAAAAAHAA LLALALLLLL LRSARALASR CASCLKTAPR RAAAVDGGLA AASSVGAWYR AALACCGYAL LAQVAALSY EVAVAGSHVA VEALLLPAVQ ALAWAALLAL AMQARAVGWG RFPVLVRVWW VVSFVLCVGI AYDDTRHLMG D DDDDEVDY ...String:
MPHFPNLPLP EAAAAAAHAA LLALALLLLL LRSARALASR CASCLKTAPR RAAAVDGGLA AASSVGAWYR AALACCGYAL LAQVAALSY EVAVAGSHVA VEALLLPAVQ ALAWAALLAL AMQARAVGWG RFPVLVRVWW VVSFVLCVGI AYDDTRHLMG D DDDDEVDY AHMVANFASA PALGFLCLVG VMGSTGVELE FTDDDSSVHE PLLLGGQRRD ADEEPGCLRV TPYGDAGIVS LA TLSWLSP LLSVGAQRPL ELADIPLMAH KDRAKSCYKA MSSHYERQRM ERPGSEPSLA WAILKSFWRE AAINGAFAAV NTI VSYVGP YLISYFVDYL SGKIEFPHEG YILASVFFVA KLLETLTARQ WYLGVDVMGI HVKSGLTAMV YRKGLRLSNS SRQS HTSGE IVNYMAVDVQ RVGDYAWYFH DIWMLPLQII LALAILYKNV GIAMVSTLVA TVLSIAASVP VAKLQEHYQD KLMAS KDER MRKTSECLKN MRILKLQAWE DRYRLKLEEM RNVECKWLRW ALYSQAAVTF VFWSSPIFVA VITFGTCILL GGELTA GGV LSALATFRIL QEPLRNFPDL ISMIAQTRVS LDRLSHFLQQ EELPDDATIT VPHGSTDKAI NINDATFSWN PSSPTPT LS GINLSVVRGM RVAVCGVIGS GKSSLLSSIL GEIPKLCGQV RISGSAAYVP QTAWIQSGNI EENILFGSPM DKQRYKRV I EACSLKKDLQ LLQYGDQTII GDRGINLSGG QKQRVQLARA LYQDADIYLL DDPFSAVDAH TGSELFREYI LTALASKTV IYVTHQIEFL PAADLILVLK DGHITQAGKY DDLLQAGTDF NALVCAHKEA IETMEFSEDS DEDTVSSVPI KRLTPSVSNI DNLKNKVSN NEKPSSTRGI KEKKKKPEER KKKRSVQEEE RERGRVSLQV YLSYMGEAYK GTLIPLIILA QTMFQVLQIA S NWWMAWAN PQTEGDAPKT DSVVLLVVYM SLAFGSSLFV FVRSLLVATF GLATAQKLFV KMLRCVFRAP MSFFDTTPSG RI LNRVSVD QSVVDLDIAF RLGGFASTTI QLLGIVAVMS KVTWQVLILI VPMAVACMWM QRYYIASSRE LTRILSVQKS PVI HLFSES IAGAATIRGF GQEKRFMKRN LYLLDCFARP LFSSLAAIEW LCLRMELLST FVFAFCMAIL VSFPPGTIEP SMAG LAVTY GLNLNARMSR WILSFCKLEN RIISVERIYQ YCKLPSEAPL IIENSRPSSS WPENGNIELV DLKVRYKDDL PLVLH GISC IFPGGKKIGI VGRTGSGKST LIQALFRLIE PTGGKVIIDD VDISRIGLHD LRSRLSIIPQ DPTLFEGTIR MNLDPL EEC TDQEIWEALE KCQLGEVIRS KDEKLDSPVL ENGDNWSVGQ RQLIALGRAL LKQAKILVLD EATASVDTAT DNLIQKI IR SEFKDCTVCT IAHRIPTVID SDLVLVLSDG KIAEFDTPQR LLEDKSSMFM QLVSEYSTRS SCI

UniProtKB: ABC transporter C family member 13

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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

BufferpH: 8 / Details: 150mM NaCl, 25mM Tris-HCL, 0.0002m/v GDN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 136844
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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