[English] 日本語
Yorodumi
- EMDB-4033: In situ atomic-resolution structure of the baseplate antenna comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4033
TitleIn situ atomic-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum obtained combining solid-state NMR spectroscopy, cryo electron microscopy and polarization spectroscopy
Map data3D reconstruction of the carotenosome CsmA-Bchl a baseplate obtained by cryo electron microscopy
Sample
  • Organelle or cellular component: Carotenosome organelle consisting of csma proteins and bchla antenna molecules.
    • Protein or peptide: Bacteriochlorophyll c-binding protein
  • Ligand: BACTERIOCHLOROPHYLL A
Keywordsphotosynthesis / light-harvesting protein / binds bacteriochlorophyll a / oligomeric complex / bacteriochlorophyll binding protein
Function / homologychlorosome envelope / Bacteriochlorophyll c-binding protein / Bacteriochlorophyll c-binding superfamily / Bacteriochlorophyll C binding protein / bacteriochlorophyll binding / photosynthesis / metal ion binding / Bacteriochlorophyll c-binding protein
Function and homology information
Biological speciesChlorobaculum tepidum (bacteria) / Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 26.5 Å
AuthorsNielsen JT / Kulminskaya NV
Funding support Denmark, Estonia, Hungary, 4 items
OrganizationGrant numberCountry
Danish National Research FoundationDNRF 59 Denmark
Estonia Research CouncilIUT02-28 Estonia
Estonian Science FoundationMJD262 Estonia
Hungarian Scientific Research FundOTKA-PD 104530 and OTKA-K 112688 Hungary
CitationJournal: Angew Chem Int Ed Engl / Year: 2012
Title: In situ solid-state NMR spectroscopy of protein in heterogeneous membranes: the baseplate antenna complex of Chlorobaculum tepidum.
Authors: Natalia V Kulminskaya / Marie Ø Pedersen / Morten Bjerring / Jarl Underhaug / Mette Miller / Niels-Ulrik Frigaard / Jakob T Nielsen / Niels Chr Nielsen /
Abstract: A clever combination: an in situ solid-state NMR analysis of CsmA proteins in the heterogeneous environment of the photoreceptor of Chlorobaculum tepidum is reported. Using different combinations of ...A clever combination: an in situ solid-state NMR analysis of CsmA proteins in the heterogeneous environment of the photoreceptor of Chlorobaculum tepidum is reported. Using different combinations of 2D and 3D solid-state NMR spectra, 90 % of the CsmA resonances are assigned and provide on the basis of chemical shift data information about the structure and conformation of CsmA in the CsmA-bacteriochlorophyll a complex.
History
DepositionJun 20, 2016-
Header (metadata) releaseJul 27, 2016-
Map releaseJul 27, 2016-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0013
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5lcb
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4033.png

Downloads & links

-
Map

FileDownload / File: emd_4033.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of the carotenosome CsmA-Bchl a baseplate obtained by cryo electron microscopy
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0013 / Movie #1: 0.0013
Minimum - Maximum-9.999734 - 13.857734000000001
Average (Standard dev.)0.00491499 (±0.9121985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin7-9-4
Dimensions256256256
Spacing256256256
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z307.200307.200307.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-97-4
NC/NR/NS256256256
D min/max/mean-10.00013.8580.005

-
Supplemental data

-
Sample components

-
Entire : Carotenosome organelle consisting of csma proteins and bchla ante...

EntireName: Carotenosome organelle consisting of csma proteins and bchla antenna molecules.
Components
  • Organelle or cellular component: Carotenosome organelle consisting of csma proteins and bchla antenna molecules.
    • Protein or peptide: Bacteriochlorophyll c-binding protein
  • Ligand: BACTERIOCHLOROPHYLL A

-
Supramolecule #1: Carotenosome organelle consisting of csma proteins and bchla ante...

SupramoleculeName: Carotenosome organelle consisting of csma proteins and bchla antenna molecules.
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Cryo-EM data of the ice-embedded isolated carotenosomes reveals molecular complex structure. Captured images clearly show supramolecular organization of the protein rows, originating from ...Details: Cryo-EM data of the ice-embedded isolated carotenosomes reveals molecular complex structure. Captured images clearly show supramolecular organization of the protein rows, originating from the BChl a - CsmA baseplate
Source (natural)Organism: Chlorobaculum tepidum (bacteria) / Organelle: carotenosome

-
Macromolecule #1: Bacteriochlorophyll c-binding protein

MacromoleculeName: Bacteriochlorophyll c-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Molecular weightTheoretical: 6.160034 KDa
Recombinant expressionOrganism: Chlorobaculum tepidum (bacteria)
SequenceString:
MSGGGVFTDI LAAAGRIFEV MVEGHWETVG MLFDSLGKGT MRINRNAYGS MGGGSLRGS

UniProtKB: Bacteriochlorophyll c-binding protein

-
Macromolecule #2: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 2 / Number of copies: 14 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/4 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 270 / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.0 µm / Calibrated defocus min: 1.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1790
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Software - details: defocus determined w ctffind3, phaseflipping w Spider
Type: PHASE FLIPPING ONLY
Startup modelType of model: OTHER / Details: Generated in Eman2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 26.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1790
Initial angle assignmentType: COMMON LINE / Software - Name: EMAN (ver. 2)
Final angle assignmentType: OTHER / Software - Name: Strul / Software - details: Ultramicroscopy 2001 87(4): 165-75
FSC plot (resolution estimation)

+
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