[English] 日本語
Yorodumi
- EMDB-38925: Sialic acid bound form of Tripartite ATP-independent Periplasmic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38925
TitleSialic acid bound form of Tripartite ATP-independent Periplasmic (TRAP) transporter from Fusobacterium nucleatum.
Map dataextracted map around pdb
Sample
  • Complex: Sialic acid bound form of TRAP transporter in 1:1 complex with its nanobody.
    • Protein or peptide: N-acetylneuraminate transporter small subunit
    • Protein or peptide: FnTRAP specific nanobody
  • Ligand: SODIUM ION
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: N-acetyl-beta-neuraminic acid
Keywordssialic acid transporter / TRAP transporter / MEMBRANE PROTEIN / TRANSPORT PROTEIN. / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homologyTRAP transporter large membrane protein DctM / TRAP C4-dicarboxylate transport system permease DctM subunit / : / Tripartite ATP-independent periplasmic transporters, DctQ component / Tripartite ATP-independent periplasmic transporter, DctM component / transmembrane transporter activity / plasma membrane / N-acetylneuraminate transporter small subunit
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsGoyal P / Ramaswamy S / Vinothkumar KR
Funding support India, 2 items
OrganizationGrant numberCountry
Other governmentIA/E/16/1/502999
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: Elife / Year: 2025
Title: Molecular determinants of Neu5Ac binding to a tripartite ATP independent periplasmic (TRAP) transporter.
Authors: Parveen Goyal / KanagaVijayan Dhanabalan / Mariafrancesca Scalise / Rosmarie Friemann / Cesare Indiveri / Renwick C J Dobson / Kutti R Vinothkumar / Subramanian Ramaswamy /
Abstract: -Acetylneuraminic acid (Neu5Ac) is a negatively charged nine-carbon amino sugar that is often the peripheral sugar in human cell-surface glycoconjugates. Some bacteria scavenge, import, and ... -Acetylneuraminic acid (Neu5Ac) is a negatively charged nine-carbon amino sugar that is often the peripheral sugar in human cell-surface glycoconjugates. Some bacteria scavenge, import, and metabolize Neu5Ac or redeploy it on their cell surfaces for immune evasion. The import of Neu5Ac by many bacteria is mediated by tripartite ATP-independent periplasmic (TRAP) transporters. We have previously reported the structures of SiaQM, a membrane-embedded component of the TRAP transport system, (Currie et al., 2024). However, none of the published structures contain Neu5Ac bound to SiaQM. This information is critical for defining the transport mechanism and for further structure-activity relationship studies. Here, we report the structures of SiaQM with and without Neu5Ac. Both structures are in an inward (cytoplasmic side) facing conformation. The Neu5Ac-bound structure reveals the interactions of Neu5Ac with the transporter and its relationship with the Na binding sites. Two of the Na-binding sites are similar to those described previously. We identify a third metal-binding site that is further away and buried in the elevator domain. Ser300 and Ser345 interact with the C1-carboxylate group of Neu5Ac. Proteoliposome-based transport assays showed that Ser300-Neu5Ac interaction is critical for transport, whereas Ser345 is dispensable. Neu5Ac primarily interacts with residues in the elevator domain of the protein, thereby supporting the elevator with an operator mechanism. The residues interacting with Neu5Ac are conserved, providing fundamental information required to design inhibitors against this class of proteins.
History
DepositionJan 31, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38925.png

Downloads & links

-
Map

FileDownload / File: emd_38925.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationextracted map around pdb
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 102 pix.
= 109.14 Å		1.07 Å/pix.
x 86 pix.
= 92.02 Å		1.07 Å/pix.
x 110 pix.
= 117.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.13
Minimum - Maximum-6.17642 - 10.029127000000001
Average (Standard dev.)0.083692156 (±0.63137466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin166158152
Dimensions86110102
Spacing10286110
CellA: 109.14001 Å / B: 92.020004 Å / C: 117.700005 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map B no mask applied

Fileemd_38925_half_map_1.map
AnnotationHalf Map B no mask applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A no mask applied

Fileemd_38925_half_map_2.map
AnnotationHalf Map A no mask applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Sialic acid bound form of TRAP transporter in 1:1 complex with it...

EntireName: Sialic acid bound form of TRAP transporter in 1:1 complex with its nanobody.
Components
  • Complex: Sialic acid bound form of TRAP transporter in 1:1 complex with its nanobody.
    • Protein or peptide: N-acetylneuraminate transporter small subunit
    • Protein or peptide: FnTRAP specific nanobody
  • Ligand: SODIUM ION
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: N-acetyl-beta-neuraminic acid

-
Supramolecule #1: Sialic acid bound form of TRAP transporter in 1:1 complex with it...

SupramoleculeName: Sialic acid bound form of TRAP transporter in 1:1 complex with its nanobody.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Fusobacterium nucleatum (bacteria)

-
Macromolecule #1: N-acetylneuraminate transporter small subunit

MacromoleculeName: N-acetylneuraminate transporter small subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 74.198938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGGSHHHHHH GSWSHPQFEK ASMTGGQQMG RDLYDDDDKD RWGSELEMKV FNKLEEWLGG SLFIGMFVIL VMQIFSRQIF NSPLIWSEE LSRLIFVYVG LLGVSMGIRS QQHIMIDFLY AKFPKSMQKI IFTIIQILIL ACLIFFLYFG YDLFIKKEEI E IVSLGISM ...String:
MGGSHHHHHH GSWSHPQFEK ASMTGGQQMG RDLYDDDDKD RWGSELEMKV FNKLEEWLGG SLFIGMFVIL VMQIFSRQIF NSPLIWSEE LSRLIFVYVG LLGVSMGIRS QQHIMIDFLY AKFPKSMQKI IFTIIQILIL ACLIFFLYFG YDLFIKKEEI E IVSLGISM KWMYLALPLI TLLMLVRFYQ AYSENYAQNK VYIKPIFILA LMIILVLIAF IKPELFKILK LSNYFDLGEM TI YYVLIAW LVMIFFGVPV GWSLLVACIL YFALTRWKVV YFAADKLVYS LDSFSLLSVP FFILTGILMN GAGITERIFN FAK AMLGHY TGGMGHVNVA ASLIFSGMSG SAIADAGGLG QLEIKAMRDE GYDDDICGGL TAASCIIGPL VPPSISMIIY GVIA NQSIA KLFLAGFVPG FLTTIALMIM NYFVCKKRGY KKTAKASPKE RWIAFKKSFW ALLTPILIIG GIFSGIFTPT EAAVI ATFY SIILGGFIYK ELTVKSFFKH CVEAVAISGV TVLMIMTVTF FGDIIAREQV AMRVAEIFIK YATSPMMVLV MINLLL LFL GMFIDALALQ FLVLPMLIPI AEQVGIDLVF FGVMTTLNMM IGILTPPMGM ALFVVAQVGK MSVSTVAKGV LPFLLPI FI TLVIITIFPQ IILFLPNLIV GG

UniProtKB: N-acetylneuraminate transporter small subunit

-
Macromolecule #2: FnTRAP specific nanobody

MacromoleculeName: FnTRAP specific nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 14.408753 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCTTSGFNFD DYAIGWFRQA PGKEREGVSC IHCTAYTPYY ARSVRDRFTI SSDNATNTVF LQMNNLRPE DTAVYYCVAD ATRYPYPEFY DYVGQGTQVT VSSHHHHHH

-
Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

-
Macromolecule #4: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 4 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

-
Macromolecule #5: N-acetyl-beta-neuraminic acid

MacromoleculeName: N-acetyl-beta-neuraminic acid / type: ligand / ID: 5 / Number of copies: 1 / Formula: SLB
Molecular weightTheoretical: 309.27 Da
Chemical component information

ChemComp-SLB:
N-acetyl-beta-neuraminic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.9 mg/mL
BufferpH: 8
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2341 / Average exposure time: 60.0 sec. / Average electron dose: 24.67 e/Å2 / Details: Of the 2341 images 1752 were used.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 130841 / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 75000
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: 653554
Startup modelType of model: INSILICO MODEL / In silico model: Using ab initio model within cryosparc
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 225006
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 6 / Avg.num./class: 53127
Details: Each class was independently refined in cryosparc. the resulting maps suggested 4 are very similar.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4572


Chain - Source name: Other / Chain - Initial model type: experimental model / Details: from the apo strcuture of the same protein
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 43.2
Output model

PDB-8y4w:
Sialic acid bound form of Tripartite ATP-independent Periplasmic (TRAP) transporter from Fusobacterium nucleatum.

+
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