[English] 日本語
Yorodumi
- EMDB-32971: Structure of a human NHE3-CHP1 complex in the autoinhibited state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32971
TitleStructure of a human NHE3-CHP1 complex in the autoinhibited state
Map data
Sample
  • Complex: Human NHE3-CHP1 complex
    • Protein or peptide: Sodium/hydrogen exchanger 3
    • Protein or peptide: Calcineurin B homologous protein 1
  • Ligand: [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{S},5~{R},6~{S})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
KeywordsSodium/proton antiporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of phosphatase activity / positive regulation of sodium:proton antiporter activity / Sodium/Proton exchangers / Hyaluronan degradation / : / membrane docking / positive regulation of protein transport / negative regulation of protein autophosphorylation / transporter complex / positive regulation of phospholipid biosynthetic process ...negative regulation of phosphatase activity / positive regulation of sodium:proton antiporter activity / Sodium/Proton exchangers / Hyaluronan degradation / : / membrane docking / positive regulation of protein transport / negative regulation of protein autophosphorylation / transporter complex / positive regulation of phospholipid biosynthetic process / potassium:proton antiporter activity / sodium:proton antiporter activity / membrane organization / microtubule bundle formation / cellular response to acidic pH / sodium ion import across plasma membrane / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of protein import into nucleus / small GTPase-mediated signal transduction / negative regulation of NF-kappaB transcription factor activity / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of protein phosphorylation / protein kinase inhibitor activity / brush border / positive regulation of protein targeting to membrane / potassium channel regulator activity / negative regulation of protein kinase activity / transport vesicle / monoatomic ion transport / cytoplasmic microtubule organization / negative regulation of protein ubiquitination / potassium ion transmembrane transport / phosphatidylinositol binding / protein export from nucleus / regulation of intracellular pH / PDZ domain binding / brush border membrane / potassium ion transport / kinase binding / recycling endosome membrane / calcium-dependent protein binding / microtubule cytoskeleton / early endosome membrane / microtubule binding / membrane fusion / early endosome / protein stabilization / apical plasma membrane / membrane raft / Golgi membrane / focal adhesion / calcium ion binding / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Na+/H+ exchanger, isoforms 3/5 / : / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Sodium/hydrogen exchanger 3 / Calcineurin B homologous protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDong Y / Li H / Gao Y / Zhang XC / Zhao Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030304 China
CitationJournal: Sci Adv / Year: 2022
Title: Structure of a human NHE3-CHP1 complex in the autoinhibited state
Authors: Dong Y / Li H / Ilie A / Gao Y / Boucher A / Zhang XC / Orlowski J / Zhao Y
History
DepositionFeb 26, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32971.png

Downloads & links

-
Map

FileDownload / File: emd_32971.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0197
Minimum - Maximum-0.1242538 - 0.2032642
Average (Standard dev.)0.00015900818 (±0.004936958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Human NHE3-CHP1 complex

EntireName: Human NHE3-CHP1 complex
Components
  • Complex: Human NHE3-CHP1 complex
    • Protein or peptide: Sodium/hydrogen exchanger 3
    • Protein or peptide: Calcineurin B homologous protein 1
  • Ligand: [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{S},5~{R},6~{S})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

-
Supramolecule #1: Human NHE3-CHP1 complex

SupramoleculeName: Human NHE3-CHP1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Sodium/hydrogen exchanger 3

MacromoleculeName: Sodium/hydrogen exchanger 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.537031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGFQVVTFEW AHVQDPYVIA LWILVASLAK IGFHLSHKVT SVVPESALLI VLGLVLGGIV WAADHIASFT LTPTVFFFYL LPPIVLDAG YFMPNRLFFG NLGTILLYAV VGTVWNAATT GLSLYGVFLS GLMGDLQIGL LDFLLFGSLM AAVDPVAVLA V FEEVHVNE ...String:
GGFQVVTFEW AHVQDPYVIA LWILVASLAK IGFHLSHKVT SVVPESALLI VLGLVLGGIV WAADHIASFT LTPTVFFFYL LPPIVLDAG YFMPNRLFFG NLGTILLYAV VGTVWNAATT GLSLYGVFLS GLMGDLQIGL LDFLLFGSLM AAVDPVAVLA V FEEVHVNE VLFIIVFGES LLNDAVTVVL YNVFESFVAL GGDNVTGVDC VKGIVSFFVV SLGGTLVGVV FAFLLSLVTR FT KHVRIIE PGFVFIISYL SYLTSEMLSL SAILAITFCG ICCQKYVKAN ISEQSATTVR YTMKMLASSA ETIIFMFLGI SAV NPFIWT WNTAFVLLTL VFISVYRAIG VVLQTWLLNR YRMVQLEPID QVVLSYGGLR GAVAFALVVL LDGDKVKEKN LFVS TTIIV VFFTVIFQGL TIKPLVQWLK VKRSEHREPR LNEKLHGRAF DHILSAIEDI SGQIGHNYLR DKWSHFDRKF LSRVL MRRS AQKSRDRILN VFHELNLKDA ISYVAEGERR GSLAFIRSPS TDNVVNVDFT PRSSTVEASV SYLLRENVSA VCLDMQ SLE QRRRSIRDAE DMVTHHTLQQ YLYKPRQEYK HLYSRHELTP TEDEKQDREI FHRTMRKRLE SFK

UniProtKB: Sodium/hydrogen exchanger 3

-
Macromolecule #2: Calcineurin B homologous protein 1

MacromoleculeName: Calcineurin B homologous protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.41191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DEELEEIKKE TGFSHSQITR LYSRFTSLDK GENGTLSRED FQRIPELAIN PLGDRIINAF FPEGEDQVNF RGFMRTLAHF RPIEDNEKS KDVNGPEPLN SRSNKLHFAF RLYDLDKDEK ISRDELLQVL RMMVGVNISD EQLGSIADRT IQEADQDGDS I ASFTEFVK VLEKVDVEQK MSIRFLH

UniProtKB: Calcineurin B homologous protein 1

-
Macromolecule #3: [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{S},5~{R},6~{S})...

MacromoleculeName: [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{S},5~{R},6~{S})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate
type: ligand / ID: 3 / Number of copies: 2 / Formula: 85R
Molecular weightTheoretical: 811.032 Da
Chemical component information

ChemComp-85R:
[(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{S},5~{R},6~{S})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate

-
Macromolecule #4: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 4 / Number of copies: 10 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 22.0 µm / Nominal defocus min: 12.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: EMDB MAP
EMDB ID:

30849

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37572
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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