[English] 日本語
Yorodumi
- EMDB-41979: R399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41979
TitleR399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed state
Map dataSharpened map
Sample
  • Organelle or cellular component: R399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed form
    • Protein or peptide: Sperm-specific sodium proton exchanger
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: Digitonin
Keywordsion transporter / SLC9 / voltage-sensor / cAMP regulated / sperm capacitation / MEMBRANE PROTEIN
Function / homology
Function and homology information


sperm head / potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / cGMP binding / sperm flagellum / single fertilization / cAMP binding / potassium ion transmembrane transport / regulation of intracellular pH ...sperm head / potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / cGMP binding / sperm flagellum / single fertilization / cAMP binding / 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, transmembrane / 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: 3.5 Å
AuthorsChowdhury S / Pal K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM145719 United States
CitationJournal: To Be Published
Title: R399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed form
Authors: Chowdhury S / Pal K
History
DepositionSep 15, 2023-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41979.png

Downloads & links

-
Map

FileDownload / File: emd_41979.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 360 pix.
= 244.8 Å		0.68 Å/pix.
x 360 pix.
= 244.8 Å		0.68 Å/pix.
x 360 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0675
Minimum - Maximum-0.41793835 - 0.66849023
Average (Standard dev.)0.0021056873 (±0.016338058)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_41979_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_41979_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41979_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : R399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed form

EntireName: R399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed form
Components
  • Organelle or cellular component: R399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed form
    • Protein or peptide: Sperm-specific sodium proton exchanger
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: Digitonin

-
Supramolecule #1: R399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed form

SupramoleculeName: R399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed form
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)

-
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: 146.650359 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 IIAG 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 V

UniProtKB: Sperm-specific sodium:proton exchanger

-
Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 3 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

-
Macromolecule #3: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 3 / Number of copies: 4 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 363742
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