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- EMDB-32971: Structure of a human NHE3-CHP1 complex in the autoinhibited state -

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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 uptake and degradation / positive regulation of protein glycosylation / membrane docking / transporter complex / negative regulation of protein autophosphorylation / positive regulation of phospholipid biosynthetic process / potassium:proton antiporter activity ...negative regulation of phosphatase activity / positive regulation of sodium:proton antiporter activity / Sodium/Proton exchangers / Hyaluronan uptake and degradation / positive regulation of protein glycosylation / membrane docking / transporter complex / negative regulation of protein autophosphorylation / positive regulation of phospholipid biosynthetic process / potassium:proton antiporter activity / positive regulation of protein transport / sodium:proton antiporter activity / membrane organization / cellular response to acidic pH / microtubule bundle formation / 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 / protein kinase inhibitor activity / negative regulation of NF-kappaB transcription factor activity / endoplasmic reticulum-Golgi intermediate compartment / brush border / negative regulation of protein phosphorylation / positive regulation of protein targeting to membrane / potassium channel regulator activity / transport vesicle / monoatomic ion transport / cytoplasmic microtubule organization / potassium ion transmembrane transport / negative regulation of protein ubiquitination / phosphatidylinositol binding / protein export from nucleus / negative regulation of protein kinase activity / PDZ domain binding / regulation of intracellular pH / brush border membrane / potassium ion transport / kinase binding / recycling endosome membrane / calcium-dependent protein binding / microtubule cytoskeleton / microtubule binding / early endosome membrane / 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-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32971.png

Downloads & links

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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 °

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Supplemental data

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Sample components

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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

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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)

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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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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

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Image processing

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

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