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- EMDB-36052: Cryo-EM structure of hZnT7DeltaHis-loop-Fab complex in zinc-unbou... -
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Open data
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Basic information
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Title | Cryo-EM structure of hZnT7DeltaHis-loop-Fab complex in zinc-unbound state, determined in outward-facing conformation | ||||||||||||
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Function / homology | ![]() zinc ion import into Golgi lumen / Golgi cis cisterna membrane / zinc ion transmembrane transporter activity / intracellular zinc ion homeostasis / sarcoplasmic reticulum membrane / cytoplasmic vesicle / vesicle / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Han BB / Inaba K / Watanabe S | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of human zinc transporter ZnT7 reveal the mechanism of Zn uptake into the Golgi apparatus. Authors: Han Ba Bui / Satoshi Watanabe / Norimichi Nomura / Kehong Liu / Tomoko Uemura / Michio Inoue / Akihisa Tsutsumi / Hiroyuki Fujita / Kengo Kinoshita / Yukinari Kato / So Iwata / Masahide Kikkawa / Kenji Inaba / ![]() Abstract: Zinc ions (Zn) are vital to most cells, with the intracellular concentrations of Zn being tightly regulated by multiple zinc transporters located at the plasma and organelle membranes. We herein ...Zinc ions (Zn) are vital to most cells, with the intracellular concentrations of Zn being tightly regulated by multiple zinc transporters located at the plasma and organelle membranes. We herein present the 2.2-3.1 Å-resolution cryo-EM structures of a Golgi-localized human Zn/H antiporter ZnT7 (hZnT7) in Zn-bound and unbound forms. Cryo-EM analyses show that hZnT7 exists as a dimer via tight interactions in both the cytosolic and transmembrane (TM) domains of two protomers, each of which contains a single Zn-binding site in its TM domain. hZnT7 undergoes a TM-helix rearrangement to create a negatively charged cytosolic cavity for Zn entry in the inward-facing conformation and widens the luminal cavity for Zn release in the outward-facing conformation. An exceptionally long cytosolic histidine-rich loop characteristic of hZnT7 binds two Zn ions, seemingly facilitating Zn recruitment to the TM metal transport pathway. These structures permit mechanisms of hZnT7-mediated Zn uptake into the Golgi to be proposed. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 45.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.8 KB 16.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 83.7 KB | ||
Masks | ![]() | 91.1 MB | ![]() | |
Others | ![]() ![]() | 84.4 MB 84.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j7xMC ![]() 8j7tC ![]() 8j7uC ![]() 8j7vC ![]() 8j7wC ![]() 8j7yC ![]() 8j80C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.18 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : Human ZnT7Delta-His-loop-Fab complex
Entire | Name: Human ZnT7Delta-His-loop-Fab complex |
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Components |
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-Supramolecule #1: Human ZnT7Delta-His-loop-Fab complex
Supramolecule | Name: Human ZnT7Delta-His-loop-Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Zinc transporter 7
Macromolecule | Name: Zinc transporter 7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.00432 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGGVAMPGAE DDVVMLPLSI KDDEYKPPKF NLFGKISGWF RSILSDKTSR NLFFFLCLNL SFAFVELLYG IWSNCLGLIS DSFHMFFDS TAILAGLAAS VISKWRDNDA FSYGYVRAEV LAGFVNGLFL IFTAFFIFSE GVERALAPPD VHHERLLLVS I LGFVVNLI ...String: MGGVAMPGAE DDVVMLPLSI KDDEYKPPKF NLFGKISGWF RSILSDKTSR NLFFFLCLNL SFAFVELLYG IWSNCLGLIS DSFHMFFDS TAILAGLAAS VISKWRDNDA FSYGYVRAEV LAGFVNGLFL IFTAFFIFSE GVERALAPPD VHHERLLLVS I LGFVVNLI GIFVFKHGGH GHSHGSGHGH SHSLFNGALD QAHGHVDHCH SHEVKHGAAH SHDHAHGHGH FHSHDGPSLK ET TGPSRQI LQGVFLHILA DTLGSIGVIA SAIMMQNFGL MIADPICSIL IAILIVVSVI PLLRESVGIL MQRTPPLLEN SLP QCYQRV QQLQGVYSLQ EQHFWTLCSD VYVGTLKLIV APDADARWIL SQTHNIFTQA GVRQLYVQID FAAM UniProtKB: ![]() |
-Macromolecule #2: Light chain of YN7114-08 Fab
Macromolecule | Name: Light chain of YN7114-08 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 24.140529 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: DIVLTQSPAS LAVSLRRRAT ISCRASESVD GYGHSFMHWY QQKSGQPPKL LIYRASNLES GVPARFSGSG SRTDFTLTID PVEADDAAT YYCQQSNEDP YTFGSGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String: DIVLTQSPAS LAVSLRRRAT ISCRASESVD GYGHSFMHWY QQKSGQPPKL LIYRASNLES GVPARFSGSG SRTDFTLTID PVEADDAAT YYCQQSNEDP YTFGSGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC |
-Macromolecule #3: Heavy chain of YN7114-08 Fab
Macromolecule | Name: Heavy chain of YN7114-08 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 24.974102 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: EVQLQESGPG LVAPSQSLSI TCTVSGFSLT NYAVHWVRQS PGKGLEWLGV IWSNGRTDYN AAFISRLSIS KDNSKSQVFF KMNSLQADD TAIYYCARKL AYEGAMDYWG QGTSVTVSSA KTTPPSVYPL APGSAAQTNS MVTLGCLVKG YFPEPVTVTW N SGSLSSGV ...String: EVQLQESGPG LVAPSQSLSI TCTVSGFSLT NYAVHWVRQS PGKGLEWLGV IWSNGRTDYN AAFISRLSIS KDNSKSQVFF KMNSLQADD TAIYYCARKL AYEGAMDYWG QGTSVTVSSA KTTPPSVYPL APGSAAQTNS MVTLGCLVKG YFPEPVTVTW N SGSLSSGV HTFPAVLQSD LYTLSSSVTV PSSTWPSETV TCNVAHPASS TKVDKKIVPR DCGCKPCICT VPEVSS |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |