[English] 日本語
Yorodumi
- EMDB-11273: Open-open state of the Bt1762-Bt1763 levan transport system -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11273
TitleOpen-open state of the Bt1762-Bt1763 levan transport system
Map dataMap filtered by local resolution
Sample
  • Complex: Dimeric Bt1762-Bt1763 levan transporter complex
    • Complex: SusD homolog
      • Protein or peptide: SusD homolog
    • Complex: SusC homolog
      • Protein or peptide: SusC homolog
KeywordsTransporter / SusCD / Levan / TonB-dependent / MEMBRANE PROTEIN
Function / homology
Function and homology information


cell outer membrane / metal ion binding
Similarity search - Function
CarboxypepD_reg-like domain / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel ...CarboxypepD_reg-like domain / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
SusC homolog / SusD homolog
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWhite JBR / van den Berg B
Funding support United Kingdom, Switzerland, 5 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P003192/1 United Kingdom
Wellcome Trust215064/Z/18/Z United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
Swiss National Science Foundation167125 Switzerland
Medical Research Council (MRC, United Kingdom)MR/N020413/1 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Insights into SusCD-mediated glycan import by a prominent gut symbiont.
Authors: Declan A Gray / Joshua B R White / Abraham O Oluwole / Parthasarathi Rath / Amy J Glenwright / Adam Mazur / Michael Zahn / Arnaud Baslé / Carl Morland / Sasha L Evans / Alan Cartmell / ...Authors: Declan A Gray / Joshua B R White / Abraham O Oluwole / Parthasarathi Rath / Amy J Glenwright / Adam Mazur / Michael Zahn / Arnaud Baslé / Carl Morland / Sasha L Evans / Alan Cartmell / Carol V Robinson / Sebastian Hiller / Neil A Ranson / David N Bolam / Bert van den Berg /
Abstract: In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport ...In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the β2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to ~2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.
History
DepositionJul 1, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zlt
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zlt
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11273.png

Downloads & links

-
Map

FileDownload / File: emd_11273.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap filtered by local resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 264 pix.
= 282.48 Å		1.07 Å/pix.
x 264 pix.
= 282.48 Å		1.07 Å/pix.
x 264 pix.
= 282.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.21110451 - 0.32315978
Average (Standard dev.)0.00023944174 (±0.0069402237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 282.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z282.480282.480282.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-0.2110.3230.000

-
Supplemental data

-
Mask #1

Fileemd_11273_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Post-processed map output from RELION

Fileemd_11273_additional_1.map
AnnotationPost-processed map output from RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: 3D refine map output from RELION

Fileemd_11273_additional_2.map
Annotation3D refine map output from RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dimeric Bt1762-Bt1763 levan transporter complex

EntireName: Dimeric Bt1762-Bt1763 levan transporter complex
Components
  • Complex: Dimeric Bt1762-Bt1763 levan transporter complex
    • Complex: SusD homolog
      • Protein or peptide: SusD homolog
    • Complex: SusC homolog
      • Protein or peptide: SusC homolog

-
Supramolecule #1: Dimeric Bt1762-Bt1763 levan transporter complex

SupramoleculeName: Dimeric Bt1762-Bt1763 levan transporter complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 360 KDa

-
Supramolecule #2: SusD homolog

SupramoleculeName: SusD homolog / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)

-
Supramolecule #3: SusC homolog

SupramoleculeName: SusC homolog / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)

-
Macromolecule #1: SusD homolog

MacromoleculeName: SusD homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Molecular weightTheoretical: 64.17816 KDa
Recombinant expressionOrganism: Bacteroides thetaiotaomicron (bacteria)
SequenceString: CDDFLDRQVP QGIVTGDQIA SPEYVDNLVI SAYAIWATGD DINSSFSLWN YDVRSDDCYK GGSGTEDGGV FNALEISKGI NTTDWNIND IWKRLYQCIT RANTALQSLD QMDEKTYPLK NQRIAEMRFL RGHAHFMLKQ LFKKIVIVND ENMEPDAYNE L SNTTYTND ...String:
CDDFLDRQVP QGIVTGDQIA SPEYVDNLVI SAYAIWATGD DINSSFSLWN YDVRSDDCYK GGSGTEDGGV FNALEISKGI NTTDWNIND IWKRLYQCIT RANTALQSLD QMDEKTYPLK NQRIAEMRFL RGHAHFMLKQ LFKKIVIVND ENMEPDAYNE L SNTTYTND EQWQKIADDF QFAYDNLPEV QIEKGRPAQA AAAAYLAKTY LYKAYRQDGA DNALTGINEE DLKQVVKYTD PL IMAKGGY GLETDYSMNF LPQYENGAES VWAIQYSIND GTYNGNLNWG MGLTTPQILG CCDFHKPSQN LVNAFKTDSQ GKP LFSTYD NENYEVATDN VDPRLFHTVG MPGFPYKYNE GYIIQKNDDW SRSKGLYGYY VSLKENVDPD CDCLKKGSYW ASSL NHIVI RYADVLLMRA EALIQLNDGR ITDAISLINE VRSRAAGSTM LIFNYKEDYG VNFKVTPYDL KAYAQDEAMK MLKWE RRVE FGMESSRFFD LVRWGEAKDV INAYYVTEAS RCSIYKNAGF TENKNEYLPV PFEQISASNG NYTQNFGWAA AAHHHH HH

UniProtKB: SusD homolog

-
Macromolecule #2: SusC homolog

MacromoleculeName: SusC homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Molecular weightTheoretical: 103.915227 KDa
SequenceString: VVVTGYTTQR KADLTGAVSV VKVDEIQKQG ENNPVKALQG RVPGMNITAD GNPSGSATVR IRGIGTLNNN DPLYIIDGVP TKAGMHELN GNDIESIQVL KDAASASIYG SRAANGVIII TTKQGKKGQI KINFDASVSA SMYQSKMNVL NTEQYGRAMW Q AYVNDGEN ...String:
VVVTGYTTQR KADLTGAVSV VKVDEIQKQG ENNPVKALQG RVPGMNITAD GNPSGSATVR IRGIGTLNNN DPLYIIDGVP TKAGMHELN GNDIESIQVL KDAASASIYG SRAANGVIII TTKQGKKGQI KINFDASVSA SMYQSKMNVL NTEQYGRAMW Q AYVNDGEN PNGNALGYAY NWGYNADGNP VLYGMTLSKY LDSKNTMPVA DTDWFDEITR TGVIQQYNLS VSNGSEKGSS FF SLGYYKN LGVIKDTDFD RFSARMNSDY KLIDDILTIG QHFTLNRTSE VQAPGGIIET ALDIPSAIPV YASDGSWGGP VGG WPDRRN PRAVLEYNKD NRYTYWRMFG DAYVNLTPFK GFNLRSTFGL DYANKQARYF TYPYQEGTQT NNGKSAVEAK QEHW TKWMW NAIATYQLEV GKHRGDVMIG MELNREDDSH FSGYKEDFSI LTPDYMWPDA GSGTAQAYGA GEGYSLVSFF GKMNY SYAD RYLLSLTLRR DGSSRFGKNH RYATFPSVSL GWRITQENFM KELTWLDDLK LRASWGQTGN QEISNLARYT IYAPNY GTT DSFGGQSYGT AYDITGSNGG GVLPSGFKRN QIGNDNIKWE TTTQTNVGID FSLFKQSLYG SLEYYYKKAT DILTEMA GV GVLGEGGSRW INSGAMKNQG FEFNLGYRNK TAFGLTYDLN GNISTYRNEI LELPETVAAN GKFGGNGVKS VVGHTYGA Q VGYIADGIFK SQDEVDNHAT QEGAAVGRIR YRDIDHNGVI DERDQNWIYD PTPSFSYGLN IYLEYKNFDL TMFWQGVQG VDIISDVKKK SDFWSASNVG FLNKGTRLLN AWSPTNPNSD IPALTRSDTN NEQRVSTYFV ENGSFLKLRN IQLGYTVPAV ISKKMRMDR LRFYCSAQNL LTIKSKNFTG EDPENPNFSY PIPVNITFGL NIGF

UniProtKB: SusC homolog

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
10.0 mMHEPES
100.0 mMSodium chlorideNaCl
0.05 % w/vLDAO
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 63.84 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Starting model was generated de novo from the data by stochastic gradient descent in RELION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 32190
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6zaz


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6zlt:
Open-open state of the Bt1762-Bt1763 levan transport system

+
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