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Yorodumi- PDB-8xom: Cryo-EM structure of human ABCC4 in complex with ANP-bound in NBD... -
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-Basic information
Entry | Database: PDB / ID: 8xom | ||||||
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Title | Cryo-EM structure of human ABCC4 in complex with ANP-bound in NBD1 and METHOTREXATE | ||||||
Components | ATP-binding cassette sub-family C member 4 | ||||||
Keywords | TRANSPORT PROTEIN / ABC transporter MRP | ||||||
Function / homology | PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-DU0 / METHOTREXATE / PALMITIC ACID / : Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å | ||||||
Authors | Zhang, P.F. / Liu, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: FEBS Lett / Year: 2024 Title: The ATP-bound inward-open conformation of ABCC4 reveals asymmetric ATP binding for substrate transport. Authors: Yue Zhu / Xiaoke Xing / Fuxing Wang / Luojun Chen / Chunhui Zhong / Xiting Lu / Zhanwang Yu / Yongbo Yang / Yi Yao / Qibin Song / Suxia Han / Zheng Liu / Pingfeng Zhang / Abstract: The multidrug resistance-associated protein (MRP) ABCC4 facilitates substrate transport across the cytoplasmic membrane, crucial for normal physiology and mediating multidrug resistance in tumor ...The multidrug resistance-associated protein (MRP) ABCC4 facilitates substrate transport across the cytoplasmic membrane, crucial for normal physiology and mediating multidrug resistance in tumor cells. Despite intensive studies on MRPs, ABCC4's transport mechanism remains incompletely understood. In this study, we unveiled an inward-open conformation with an ATP bound to degenerate NBD1. Additionally, we captured the structure with both ATP and substrate co-bound in the inward-open state. Our findings uncover the asymmetric ATP binding in ABCC4 and provide insights into substrate binding and transport mechanisms. ATP binding to NBD1 is parallel to substrate binding to ABCC4, and is a prerequisite for ATP-bound NBD2-induced global conformational changes. Our findings shed new light on targeting ABCC4 in combination with anticancer therapy. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xom.cif.gz | 329.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xom.ent.gz | 213.2 KB | Display | PDB format |
PDBx/mmJSON format | 8xom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xom_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8xom_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8xom_validation.xml.gz | 53.6 KB | Display | |
Data in CIF | 8xom_validation.cif.gz | 77 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/8xom ftp://data.pdbj.org/pub/pdb/validation_reports/xo/8xom | HTTPS FTP |
-Related structure data
Related structure data | 38534MC 8xokC 8xolC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 149693.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABCC4 Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) References: UniProt: O15439, ABC-type xenobiotic transporter, ABC-type glutathione-S-conjugate transporter |
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-Non-polymers , 5 types, 18 molecules
#2: Chemical | ChemComp-ANP / | ||||
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#3: Chemical | ChemComp-MTX / | ||||
#4: Chemical | ChemComp-DU0 / #5: Chemical | ChemComp-PLM / | #6: Chemical | ChemComp-MG / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human ABCC4 in complex with ANP-bound in NBD1 and MTX / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.1495 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) |
Buffer solution | pH: 7.5 Details: 50 mM HEPES pH 7.5, 150 mM NaCl, 2 mM DTT, 2 mM MgCl2, 0.005% (w/v) GDN and 0.0005% CHS |
Buffer component | Conc.: 25 mM / Name: Hepes |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The human ABCC4 protein was purified in 0.005% (w/v) GDN and 0.0005% CHS, the peak protein fraction from gel filtration column were concentrated to about 10 mg/ml. |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: After incubation on the grids at 277K under 100% humidity for 10 s, the grids were bloted for 3.0 s and then plunged frozen into liquid ethane cooled by liquid nitrogen using a Vitrobot. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: SerialEM / Category: image acquisition | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5036677 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1283813 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 195.99 Å2 | ||||||||||||||||||||||||
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