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- PDB-8ipq: Cryo-EM structure of heme transporter CydDC from Mycobacterium sm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ipq | ||||||||||||||||||
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Title | Cryo-EM structure of heme transporter CydDC from Mycobacterium smegmatis in the inward facing apo state | ||||||||||||||||||
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![]() | TRANSPORT PROTEIN / ABC transporter / Heme | ||||||||||||||||||
Function / homology | ![]() sulfate-transporting ATPase / cysteine transport / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
![]() | Zhu, C. / Li, J. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 326.1 KB | Display | ![]() |
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PDB format | ![]() | 262.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 64.2 KB | Display | |
Data in CIF | ![]() | 95 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35640MC ![]() 8iprC ![]() 8ipsC ![]() 8iptC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Components
#1: Protein | Mass: 53259.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: A0A8B4R4Z5, sulfate-transporting ATPase #2: Protein | Mass: 54821.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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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 |
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Sample preparation
Component | Name: CydDC / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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) |
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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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107090 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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