[English] 日本語
Yorodumi
- PDB-8ips: Cryo-EM structure of heme transporter CydDC from Escherichia coli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ips
TitleCryo-EM structure of heme transporter CydDC from Escherichia coli in the inward facing heme loading state
Components
  • ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC
  • ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD
KeywordsTRANSPORT PROTEIN / ABC transporter / Heme
Function / homology
Function and homology information


cysteine transport / glutathione transmembrane transport / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / cell redox homeostasis / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / Type 1 protein exporter / 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, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / Type 1 protein exporter / 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
PROTOPORPHYRIN IX CONTAINING FE / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhu, C. / Li, J.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1300900 China
Ministry of Science and Technology (MoST, China)22ZR1441600 China
Other government22ZR1441600
Other governmentZD2021CY1001
Other governmentLG202101-01-08 China
CitationJournal: 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
DepositionMar 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC
B: ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,5643
Polymers129,9482
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC


Mass: 64802.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria)
Gene: ECBD_2709
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A140NDD5
#2: Protein ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD


Mass: 65144.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria)
Gene: ECBD_2708
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A140NDK4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: CydDC / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146840 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039207
ELECTRON MICROSCOPYf_angle_d0.59712508
ELECTRON MICROSCOPYf_dihedral_angle_d4.4621267
ELECTRON MICROSCOPYf_chiral_restr0.0391456
ELECTRON MICROSCOPYf_plane_restr0.0051603

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more