[English] 日本語
Yorodumi
- EMDB-17185: Cryo-EM structure of Strongylocentrotus purpuratus SLC9C1 in pres... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17185
TitleCryo-EM structure of Strongylocentrotus purpuratus SLC9C1 in presence of cAMP
Map data
Sample
  • Complex: Homo-dimer of SLC9C1 transporter
    • Protein or peptide: Sperm-specific sodium proton exchanger
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsVSD / CNBD / Transporter / Voltage sensor / exchanger / sperm motility / cAMP binding / TRANSPORT PROTEIN
Function / homology
Function and homology information


potassium:proton antiporter activity / sperm head / sodium:proton antiporter activity / sodium ion import across plasma membrane / cGMP binding / single fertilization / sperm flagellum / cAMP binding / cAMP-mediated signaling / potassium ion transmembrane transport ...potassium:proton antiporter activity / sperm head / sodium:proton antiporter activity / sodium ion import across plasma membrane / cGMP binding / single fertilization / sperm flagellum / cAMP binding / cAMP-mediated signaling / potassium ion transmembrane transport / regulation of intracellular pH / protein homodimerization activity / plasma membrane
Similarity search - Function
Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Voltage-dependent channel domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Sperm-specific sodium:proton exchanger
Similarity search - Component
Biological speciesStrongylocentrotus purpuratus (purple sea urchin)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsYeo H / Mehta V / Gulati A / Drew D
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-820187European Union
CitationJournal: Nature / Year: 2023
Title: Structure and electromechanical coupling of a voltage-gated Na/H exchanger.
Authors: Hyunku Yeo / Ved Mehta / Ashutosh Gulati / David Drew /
Abstract: Voltage-sensing domains control the activation of voltage-gated ion channels, with a few exceptions. One such exception is the sperm-specific Na/H exchanger SLC9C1, which is the only known ...Voltage-sensing domains control the activation of voltage-gated ion channels, with a few exceptions. One such exception is the sperm-specific Na/H exchanger SLC9C1, which is the only known transporter to be regulated by voltage-sensing domains. After hyperpolarization of sperm flagella, SLC9C1 becomes active, causing pH alkalinization and CatSper Ca channel activation, which drives chemotaxis. SLC9C1 activation is further regulated by cAMP, which is produced by soluble adenyl cyclase (sAC). SLC9C1 is therefore an essential component of the pH-sAC-cAMP signalling pathway in metazoa, required for sperm motility and fertilization. Despite its importance, the molecular basis of SLC9C1 voltage activation is unclear. Here we report cryo-electron microscopy (cryo-EM) structures of sea urchin SLC9C1 in detergent and nanodiscs. We show that the voltage-sensing domains are positioned in an unusual configuration, sandwiching each side of the SLC9C1 homodimer. The S4 segment is very long, 90 Å in length, and connects the voltage-sensing domains to the cytoplasmic cyclic-nucleotide-binding domains. The S4 segment is in the up configuration-the inactive state of SLC9C1. Consistently, although a negatively charged cavity is accessible for Na to bind to the ion-transporting domains of SLC9C1, an intracellular helix connected to S4 restricts their movement. On the basis of the differences in the cryo-EM structure of SLC9C1 in the presence of cAMP, we propose that, upon hyperpolarization, the S4 segment moves down, removing this constriction and enabling Na/H exchange.
History
DepositionApr 21, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17185.png

Downloads & links

-
Map

FileDownload / File: emd_17185.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 320 pix.
= 318.944 Å		1 Å/pix.
x 320 pix.
= 318.944 Å		1 Å/pix.
x 320 pix.
= 318.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9967 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.20150876 - 0.4112946
Average (Standard dev.)0.00018168056 (±0.01224313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 318.944 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_17185_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_17185_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_17185_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homo-dimer of SLC9C1 transporter

EntireName: Homo-dimer of SLC9C1 transporter
Components
  • Complex: Homo-dimer of SLC9C1 transporter
    • Protein or peptide: Sperm-specific sodium proton exchanger
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

-
Supramolecule #1: Homo-dimer of SLC9C1 transporter

SupramoleculeName: Homo-dimer of SLC9C1 transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
Molecular weightTheoretical: 294.733 KDa

-
Macromolecule #1: Sperm-specific sodium proton exchanger

MacromoleculeName: Sperm-specific sodium proton exchanger / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
Molecular weightTheoretical: 147.531328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKKRVVKLRE LVPAVAALAV AVLIQSATGS SGGSGHTPTT QATHADDHDL TTHNGTEEHD DGHDDGHDDL HAHAPKVIVF ISGSCLFGA ISRSLFKKLP IPYTVVLLIL GAILGVVASN VPLVEEHTRD VAHMDPHVLL QIFLPVLIFE SAFAMDVHTF M RSFSQVCI ...String:
MKKRVVKLRE LVPAVAALAV AVLIQSATGS SGGSGHTPTT QATHADDHDL TTHNGTEEHD DGHDDGHDDL HAHAPKVIVF ISGSCLFGA ISRSLFKKLP IPYTVVLLIL GAILGVVASN VPLVEEHTRD VAHMDPHVLL QIFLPVLIFE SAFAMDVHTF M RSFSQVCI LALFGLVVAS VLTAVLAMNL FNYNWNFSEA MMFGAIMSAT DPVAVVALLK DLGASKQLGT IIEGESLLND GC AIVIFNV FMKMVFFPQL TSTVGQNVLY FLQVAVAGPL WGYAVAKVTV FFLSHIFNDA LVEITITLAA TYLTYYIGDI WLE VSGVLA VVVLGLIVNA EKTSISPEVE VFLHRFWEML AYLANTLIFM MVGVVVTQKA LVAVDKMDWF YLIILYLAIT IIRG MVISL FSPILSRIGY GLTWRNAVIM TWGGLRGAVG LALALVVENL AGNDVIGSKF LFHTAGIVVL TLVINATTIQ TLLRI LGMS DISIPKRLAM AGAVRRIHEG QNRTLNMLKS DRFLADADWD IATAACEISD PYSALSDDEN APADELTLGE RKSVCP GCK AMVPNEPSPR EFADMMEEAR LRMLKAEKIS YWKQFEHGML AREALRLLVQ HAEVAADEKD QFILVDDLKK SWQIKGI YP WLKRKLEDLI SEKKIAAIPM PKYKLGKLMY KICHHMAFEV TINIAIVLNI VPIIMEFVVQ DKMASVSTMA APGSTVSS E PSSLQKIEDA LRISNYVFFV IYAIEAIVKI LGLGRHYIVS HWNKFDAFIL VVALVDIIIA ETLLKGSITI NLSSIKVVK LFRLLRGLRM LRLTKALIPK LILVVNGKIN NQLSLGYDVG KGYIIGEEEV GKIIDRMVDN KKILRELKHI SETGRLQVVK ELGLLQREH PGIAVSVKTR QAIRTILNHS RETIHELQGA GLLDEMEAHK LELTVEIKMK RLMNAPSSIP PPPPENLLKN V SWLAGDMK LIDFIKARAS LLHFDYGEVI VREGDESDGL FLIVSGLVKL YGKSAFLDHD NPPVTAGSEE NEVFEDYLTV GN VIGEMGV LTKKPRNATV TCETTVQVYF ITAEDMNIAI DTFTLYPSLE YRLWRVVAIR IATPLIMEQM AFQGWTQEKV KLH LERGYL VDLAESHFQF NIDATLEDVI LINGTAYNAH TREEIRSPCL ISRTVHKLTF QYTATEEPRL FVVRNAEYNG PILD GRLDV DSKRSLISIT EISSNMCLKH AAELRQKNSK VMLSRKSSGA AAKEEEDCIP NTSDVEQAAG VSPSVPTKTT PKPKS FLPS LGLSMSKERV NGEAVEESPV KTKQGEETPE TEEGAAPRVN VENLYFQ

UniProtKB: Sperm-specific sodium:proton exchanger

-
Macromolecule #2: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.21 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94091
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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