[English] 日本語
Yorodumi
- EMDB-24942: Helicobacter Hepaticus CcsBA Closed Conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24942
TitleHelicobacter Hepaticus CcsBA Closed Conformation
Map data
Sample
  • Complex: Complex of CcsBA with one heme present
    • Protein or peptide: Cytochrome c biogenesis protein
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: HEME B/C
Function / homologyResB-like domain / ResB-like family / Cytochrome c-type biogenesis protein CcsA/CcmC / Cytochrome c assembly protein / Cytochrome C assembly protein / cytochrome complex assembly / heme binding / plasma membrane / Cytochrome c biogenesis protein
Function and homology information
Biological speciesHelicobacter hepaticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 Å
AuthorsMendez DL / Lowder EP / Tillman DE / Sutherland MC / Collier AL / Rau MJ / Fitzpatrick JA / Kranz RG
Funding support5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM47909
Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital2015-505
Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital2019-813
Foundation for Barnes-Jewish Hospital3770
Chan Zuckerberg Initiative2020-225726
CitationJournal: Nat Chem Biol / Year: 2022
Title: Cryo-EM of CcsBA reveals the basis for cytochrome c biogenesis and heme transport.
Authors: Deanna L Mendez / Ethan P Lowder / Dustin E Tillman / Molly C Sutherland / Andrea L Collier / Michael J Rau / James A J Fitzpatrick / Robert G Kranz /
Abstract: Although the individual structures and respiratory functions of cytochromes are well studied, the structural basis for their assembly, including transport of heme for attachment, are unknown. We ...Although the individual structures and respiratory functions of cytochromes are well studied, the structural basis for their assembly, including transport of heme for attachment, are unknown. We describe cryo-electron microscopy (cryo-EM) structures of CcsBA, a bifunctional heme transporter and cytochrome c (cyt c) synthase. Models built from the cryo-EM densities show that CcsBA is trapped with heme in two conformations, herein termed the closed and open states. The closed state has heme located solely at a transmembrane (TM) site, with a large periplasmic domain oriented such that access of heme to the cytochrome acceptor is denied. The open conformation contains two heme moieties, one in the TM-heme site and another in an external site (P-heme site). The presence of heme in the periplasmic site at the base of a chamber induces a large conformational shift that exposes the heme for reaction with apocytochrome c (apocyt c). Consistent with these structures, in vivo and in vitro cyt c synthase studies suggest a mechanism for transfer of the periplasmic heme to cytochrome.
History
DepositionSep 21, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateJan 12, 2022-
Current statusJan 12, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7s9z
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24942.png

Downloads & links

-
Map

FileDownload / File: emd_24942.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.178 / Movie #1: 0.18
Minimum - Maximum-0.5655987 - 0.98931783
Average (Standard dev.)0.00094300817 (±0.020394256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.5660.9890.001

-
Supplemental data

-
Sample components

-
Entire : Complex of CcsBA with one heme present

EntireName: Complex of CcsBA with one heme present
Components
  • Complex: Complex of CcsBA with one heme present
    • Protein or peptide: Cytochrome c biogenesis protein
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: HEME B/C

-
Supramolecule #1: Complex of CcsBA with one heme present

SupramoleculeName: Complex of CcsBA with one heme present / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Purified from E. coli in DDM
Source (natural)Organism: Helicobacter hepaticus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: C43 / Recombinant plasmid: pGEX

-
Macromolecule #1: Cytochrome c biogenesis protein

MacromoleculeName: Cytochrome c biogenesis protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter hepaticus (bacteria)
Molecular weightTheoretical: 107.291469 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MMNIIKTLFC SMKMVLLLIG IYATACGIAT FIEKYEGTLA ARLWVYDAFW FEILHIWLVA CLIGCFITSK AWQRKKYASL LLHASFIVI IIGAGITRYY GFEGLMNLRE GQSVNFISTN THYIFIQIKN PQGDVESVRI PTYIDEKVNH KINQHLTFFG K PLTLHTEE ...String:
MMNIIKTLFC SMKMVLLLIG IYATACGIAT FIEKYEGTLA ARLWVYDAFW FEILHIWLVA CLIGCFITSK AWQRKKYASL LLHASFIVI IIGAGITRYY GFEGLMNLRE GQSVNFISTN THYIFIQIKN PQGDVESVRI PTYIDEKVNH KINQHLTFFG K PLTLHTEE FTAKQVNMSE LFILNASIDF LGKNEKTLIM RDGNNAPTKE NITMLEIEGY KIFLAWGIDN IALPFSIKLK KF ELERYPG SNSPASYTSE VEVLDGQNPP LPFRIFMNNV LDYGGYRFFQ SSYHPDEKGS ILSVNNDPGK TPTYIGYAML ILG VIWLLF DKNGRFATLG RFLKTQKFFS LMLCSALCYA LSSPQIAYAS TQSQTDFQPL SENEIPPLQD IPSMIKALAD TSSL TNDFD RILVQDFGGR IKPMHTLANE YIHKLTQQRT FKGLNPSQVF LGMLFYPQEW QSIQMIATKS PKLRQILGLD ENQKH IAYI DVFTPQGQYI LQNYVEAANL KSPSLRDTFE KDVISVDERI NYAFLIYTGQ VLRIFPDNKS PNNQWLYPLQ AISSAV AQD DTKKAKELMQ IYKKFAQGMQ QGINTHNWQE AAQATRDIRT FQQNNGGSLL ISPAKVDSEI WLNLYNPFYQ LTYPYIF IS IVLFIIVLVG ILKNTPTRPL IHKVFYILLF ALFILHTCGL GLRWYVSEHA PWSNAYESML YIAWAAILSG VVFFRRSN L ALCASSFLAG MTLFVANLGD MDPQIGNLMP VLKSYWLNIH VSVITASYGF LGLCFMLGLI TLIMFLLRNE KRSQVDCSI LSLSALNEMS MILGLFLLSV GNFLGGIWAN ESWGRYWGWD SKETWALISI GVYAIILHLR FVVPKNFPFI FASASVIGFF SVLMTYFGV NYYLTGMHSY AAGEAEPVPL WVELMVAGII LLIIIASRKR VLDMPHLHHH HHH

-
Macromolecule #2: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

-
Macromolecule #3: HEME B/C

MacromoleculeName: HEME B/C / type: ligand / ID: 3 / Number of copies: 1 / Formula: HEB
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEB:
HEME B/C

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
100.0 mMNaCLSodium chlorideSodium chloride
0.03 %C24H46O11DDM
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.009300000000000001 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot for 2 seconds at a blot force of -1 and plunge frozen.

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsSpherical aberration corrector: Microscope is outfitted with a Cs image corrector with two hexapole elements.
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV / Details: Specific energy filter was a Gatan BioQuantum 968.
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 82.0 K / Max: 84.0 K
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3832 pixel / Digitization - Dimensions - Height: 3704 pixel / Number grids imaged: 1 / Number real images: 8676 / Average exposure time: 8.0 sec. / Average electron dose: 66.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1778157
Details: Initial particle picking was facilitated using the blob picker in cryoSPARC. Picked particles were then subjected to 2D classification. Once converged, a sub-set of 2D classes were manually ...Details: Initial particle picking was facilitated using the blob picker in cryoSPARC. Picked particles were then subjected to 2D classification. Once converged, a sub-set of 2D classes were manually picked and reclassified using a smaller number of classes.
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2)
Startup modelType of model: INSILICO MODEL
In silico model: Initial model was created using the ab initio method in cryoSPARC v3.2
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final 3D classificationNumber classes: 4 / Avg.num./class: 72000 / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 117488

-
Atomic model buiding 1

DetailsModel was built de novo into density map using COOT. Both Phenix and ISOLDE were used for refinement
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7s9z:
Helicobacter Hepaticus CcsBA Closed Conformation

+
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