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Yorodumi- PDB-8ipr: Cryo-EM structure of heme transporter CydDC from Mycobacterium sm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ipr | ||||||||||||||||||
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Title | Cryo-EM structure of heme transporter CydDC from Mycobacterium smegmatis in the outward facing ATP bound state | ||||||||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN / ABC transporter / Heme | ||||||||||||||||||
Function / homology | Function and homology information sulfate-transporting ATPase / cysteine transport / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||||||||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||||||||||||||
Authors | Zhu, C. / Li, J. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Protein Cell / Year: 2023 Title: Cryo-EM structures of a prokaryotic heme transporter CydDC. Authors: Chen Zhu / Yanfeng Shi / Jing Yu / Wenhao Zhao / Lingqiao Li / Jingxi Liang / Xiaolin Yang / Bing Zhang / Yao Zhao / Yan Gao / Xiaobo Chen / Xiuna Yang / Lu Zhang / Luke W Guddat / Lei Liu / ...Authors: Chen Zhu / Yanfeng Shi / Jing Yu / Wenhao Zhao / Lingqiao Li / Jingxi Liang / Xiaolin Yang / Bing Zhang / Yao Zhao / Yan Gao / Xiaobo Chen / Xiuna Yang / Lu Zhang / Luke W Guddat / Lei Liu / Haitao Yang / Zihe Rao / Jun Li / | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ipr.cif.gz | 372.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ipr.ent.gz | 298.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ipr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ipr_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8ipr_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8ipr_validation.xml.gz | 65.6 KB | Display | |
Data in CIF | 8ipr_validation.cif.gz | 95.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/8ipr ftp://data.pdbj.org/pub/pdb/validation_reports/ip/8ipr | HTTPS FTP |
-Related structure data
Related structure data | 35641MC 8ipqC 8ipsC 8iptC 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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2 |
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-Components
#1: Protein | Mass: 51880.230 Da / Num. of mol.: 2 / Mutation: E458Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: cydC / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A8B4R833 #2: Protein | Mass: 53259.000 Da / Num. of mol.: 2 / Mutation: E456Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: cydD, NCTC7017_05649 / Production host: Mycolicibacterium smegmatis (bacteria) References: UniProt: A0A8B4R4Z5, sulfate-transporting ATPase #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ATP / Has ligand of interest | N | |
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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: CydDC / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) |
Source (recombinant) | Organism: Mycolicibacterium smegmatis (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158908 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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