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Yorodumi- EMDB-32971: Structure of a human NHE3-CHP1 complex in the autoinhibited state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32971 | |||||||||
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Title | Structure of a human NHE3-CHP1 complex in the autoinhibited state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Sodium/proton antiporter / MEMBRANE PROTEIN | |||||||||
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 / positive regulation of phospholipid biosynthetic process / negative regulation of protein autophosphorylation / potassium:proton antiporter activity ...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 / positive regulation of phospholipid biosynthetic process / negative regulation of protein autophosphorylation / potassium:proton antiporter activity / 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 / transport vesicle / potassium ion transmembrane transport / negative regulation of protein ubiquitination / protein export from nucleus / negative regulation of protein phosphorylation / PDZ domain binding / regulation of intracellular pH / brush border membrane / negative regulation of protein kinase activity / potassium ion transport / kinase binding / calcium-dependent protein binding / microtubule cytoskeleton / microtubule binding / membrane => GO:0016020 / membrane fusion / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Dong Y / Li H / Gao Y / Zhang XC / Zhao Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32971.map.gz | 5.6 MB | EMDB map data format | |
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Header (meta data) | emd-32971-v30.xml emd-32971.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | emd_32971.png | 94.6 KB | ||
Filedesc metadata | emd-32971.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32971 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32971 | HTTPS FTP |
-Validation report
Summary document | emd_32971_validation.pdf.gz | 375.7 KB | Display | EMDB validaton report |
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Full document | emd_32971_full_validation.pdf.gz | 375.3 KB | Display | |
Data in XML | emd_32971_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | emd_32971_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32971 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32971 | HTTPS FTP |
-Related structure data
Related structure data | 7x2uMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32971.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Human NHE3-CHP1 complex
Entire | Name: Human NHE3-CHP1 complex |
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Components |
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-Supramolecule #1: Human NHE3-CHP1 complex
Supramolecule | Name: Human NHE3-CHP1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Sodium/hydrogen exchanger 3
Macromolecule | Name: Sodium/hydrogen exchanger 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 70.537031 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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
Macromolecule | Name: Calcineurin B homologous protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 21.41191 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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})...
Macromolecule | Name: [(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 |
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Molecular weight | Theoretical: 811.032 Da |
Chemical component information | ChemComp-85R: |
-Macromolecule #4: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
Macromolecule | Name: (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 |
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Molecular weight | Theoretical: 751.023 Da |
Chemical component information | ChemComp-PGT: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37572 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |