[English] 日本語
Yorodumi
- EMDB-60316: Cryo-EM structure of bicarbonate transporter SbtA in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60316
TitleCryo-EM structure of bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB (T-loop truncation) from Synechocystis sp. PCC 6803
Map datasbtAB
Sample
  • Complex: Bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB (T-loop truncation)
    • Protein or peptide: Slr1512 protein
    • Protein or peptide: Membrane-associated protein slr1513
  • Ligand: BICARBONATE ION
KeywordsComplex / T-loop truncation / TRANSPORT PROTEIN
Function / homology
Function and homology information


regulation of nitrogen utilization / plasma membrane-derived thylakoid membrane / enzyme regulator activity / membrane
Similarity search - Function
Na+-dependent bicarbonate transporter superfamily / Na+-dependent bicarbonate transporter superfamily / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal
Similarity search - Domain/homology
Slr1512 protein / Membrane-associated protein slr1513
Similarity search - Component
Biological speciesSynechocystis (bacteria) / Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHou WT / Zhou CZ
Funding support China, 2 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020301 China
Chinese Academy of SciencesXDA24020302 China
CitationJournal: To Be Published
Title: Cryo-EM structure of bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB T-loop truncation from Synechocystis sp. PCC 6803
Authors: Hou WT / Zhou CZ
History
DepositionMay 29, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60316.png

Downloads & links

-
Map

FileDownload / File: emd_60316.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationsbtAB
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 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: 0.262
Minimum - Maximum-1.4093416 - 2.2330105
Average (Standard dev.)0.0015754655 (±0.059167713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_60316_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60316_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bicarbonate transporter SbtA in complex with PII-like signaling p...

EntireName: Bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB (T-loop truncation)
Components
  • Complex: Bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB (T-loop truncation)
    • Protein or peptide: Slr1512 protein
    • Protein or peptide: Membrane-associated protein slr1513
  • Ligand: BICARBONATE ION

-
Supramolecule #1: Bicarbonate transporter SbtA in complex with PII-like signaling p...

SupramoleculeName: Bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB (T-loop truncation)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Synechocystis (bacteria)

-
Macromolecule #1: Slr1512 protein

MacromoleculeName: Slr1512 protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 39.671246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDFLSNFLTD FVGQLQSPTL AFLIGGMVIA ALGTQLVIPE AISTIIVFML LTKIGLTGGM AIRNSNLTEM LLPVAFSVIL GILIVFIAR FTLAKLPNVR TVDALATGGL FGAVSGSTMA AALTTLEESK ISYEAWAGAL YPFMDIPALV TAIVVANIYL N KRKRKSAA ...String:
MDFLSNFLTD FVGQLQSPTL AFLIGGMVIA ALGTQLVIPE AISTIIVFML LTKIGLTGGM AIRNSNLTEM LLPVAFSVIL GILIVFIAR FTLAKLPNVR TVDALATGGL FGAVSGSTMA AALTTLEESK ISYEAWAGAL YPFMDIPALV TAIVVANIYL N KRKRKSAA ASIEESFSKQ PVAAGDYGDQ TDYPRTRQEY LSQQEPEDNR VKIWPIIEES LQGPALSAML LGLALGIFTK PE SVYEGFY DPLFRGLLSI LMLIMGMEAW SRIGELRKVA QWYVVYSLIA PIVHGFIAFG LGMIAHYATG FSLGGVVVLA VIA ASSSDI SGPPTLRAGI PSANPSAYIG SSTAIGTPIA IGVCIPLFIG LAQTLGAG

UniProtKB: Slr1512 protein

-
Macromolecule #2: Membrane-associated protein slr1513

MacromoleculeName: Membrane-associated protein slr1513 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 12.02181 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKPANKLVI VTEKILLKKI AKIIDESGAK GYTVMNTGGK GSRNVRSSGQ PNTSDIEANI KFEILTETRE MAEEIADRVA VKYFNDYAG IIYICSAEVL YGHTFCGPEG C

UniProtKB: Membrane-associated protein slr1513

-
Macromolecule #3: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7cyf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178612
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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