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

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ID or keywords:

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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
Function / homology
Function and homology information


positive regulation of sodium:proton antiporter activity / Sodium/Proton exchangers / negative regulation of phosphatase activity / transporter complex / positive regulation of protein glycosylation / Hyaluronan uptake and degradation / membrane docking / potassium:proton antiporter activity / positive regulation of phospholipid biosynthetic process / negative regulation of protein autophosphorylation ...positive regulation of sodium:proton antiporter activity / Sodium/Proton exchangers / negative regulation of phosphatase activity / transporter complex / positive regulation of protein glycosylation / Hyaluronan uptake and degradation / membrane docking / potassium:proton antiporter activity / positive regulation of phospholipid biosynthetic process / negative regulation of protein autophosphorylation / sodium:proton antiporter activity / positive regulation of protein transport / cellular response to acidic pH / membrane organization / sodium ion import across plasma membrane / microtubule bundle formation / 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 / protein kinase inhibitor activity / brush border / endoplasmic reticulum-Golgi intermediate compartment / potassium channel regulator activity / positive regulation of protein targeting to membrane / monoatomic ion transport / cytoplasmic microtubule organization / potassium ion transmembrane transport / transport vesicle / negative regulation of protein ubiquitination / protein export from nucleus / negative regulation of protein phosphorylation / PDZ domain binding / brush border membrane / regulation of intracellular pH / negative regulation of protein kinase activity / potassium ion transport / kinase binding / calcium-dependent protein binding / microtubule cytoskeleton / microtubule binding / membrane fusion / membrane => GO:0016020 / protein stabilization / membrane raft / apical plasma membrane / Golgi membrane / focal adhesion / calcium ion binding / cell surface / endoplasmic reticulum / extracellular exosome / 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 family / 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-
UpdateApr 27, 2022-
Current statusApr 27, 2022Processing 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)
Voxel sizeX=Y=Z: 1 Å
Density
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 / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293

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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

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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

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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 / Phosphatidylglycerol

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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

30849

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

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