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Yorodumi- EMDB-24784: Cryo-EM map of human GlcNAc-1-phosphotransferase A2B2 subcomplex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24784 | |||||||||
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Title | Cryo-EM map of human GlcNAc-1-phosphotransferase A2B2 subcomplex | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase / N-glycan processing to lysosome / secretion of lysosomal enzymes / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / carbohydrate phosphorylation / lysosome organization / establishment of localization in cell / Golgi membrane / calcium ion binding / Golgi apparatus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Li H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Structure of the human GlcNAc-1-phosphotransferase αβ subunits reveals regulatory mechanism for lysosomal enzyme glycan phosphorylation. Authors: Hua Li / Wang-Sik Lee / Xiang Feng / Lin Bai / Benjamin C Jennings / Lin Liu / Balraj Doray / William M Canfield / Stuart Kornfeld / Huilin Li / Abstract: Vertebrates use the mannose 6-phosphate (M6P)-recognition system to deliver lysosomal hydrolases to lysosomes. Key to this pathway is N-acetylglucosamine (GlcNAc)-1-phosphotransferase (PTase) that ...Vertebrates use the mannose 6-phosphate (M6P)-recognition system to deliver lysosomal hydrolases to lysosomes. Key to this pathway is N-acetylglucosamine (GlcNAc)-1-phosphotransferase (PTase) that selectively adds GlcNAc-phosphate (P) to mannose residues of hydrolases. Human PTase is an αβγ heterohexamer with a catalytic core and several peripheral domains that recognize and bind substrates. Here we report a cryo-EM structure of the catalytic core of human PTase and the identification of a hockey stick-like motif that controls activation of the enzyme. Movement of this motif out of the catalytic pocket is associated with a rearrangement of part of the peripheral domains that unblocks hydrolase glycan access to the catalytic site, thereby activating PTase. We propose that PTase fluctuates between inactive and active states in solution, and selective substrate binding of a lysosomal hydrolase through its protein-binding determinant to PTase locks the enzyme in the active state to permit glycan phosphorylation. This mechanism would help ensure that only N-linked glycans of lysosomal enzymes are phosphorylated. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24784.map.gz | 117.7 MB | EMDB map data format | |
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Header (meta data) | emd-24784-v30.xml emd-24784.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24784_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_24784.png | 164.2 KB | ||
Others | emd_24784_half_map_1.map.gz emd_24784_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24784 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24784 | HTTPS FTP |
-Related structure data
Related structure data | 7s05MC 7s06C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24784.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_24784_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_24784_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GlcNAc-1-phosphotransferase
Entire | Name: GlcNAc-1-phosphotransferase |
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Components |
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-Supramolecule #1: GlcNAc-1-phosphotransferase
Supramolecule | Name: GlcNAc-1-phosphotransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
-Macromolecule #1: N-acetylglucosamine-1-phosphotransferase subunits alpha/beta
Macromolecule | Name: N-acetylglucosamine-1-phosphotransferase subunits alpha/beta type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 134.7875 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DEDQVDPRLI DGKWSRDQYH VLFDSYRDNI AGKSFQNRLC LPMPIDVVYT WVNGTDLELL KELQQVREQM EEEQKAMREI LGKNTTEPT KKSEKQLECL LTHCIKVPML VLDPALPANI TLKDLPSLYP SFHSASDIFN VAKPKNPSTN VSVVVFDSTK D VEDAHSGL ...String: DEDQVDPRLI DGKWSRDQYH VLFDSYRDNI AGKSFQNRLC LPMPIDVVYT WVNGTDLELL KELQQVREQM EEEQKAMREI LGKNTTEPT KKSEKQLECL LTHCIKVPML VLDPALPANI TLKDLPSLYP SFHSASDIFN VAKPKNPSTN VSVVVFDSTK D VEDAHSGL LKGNSRQTVW RGYLTTDKEV PGLVLMQDLA FLSGFPPTFK ETNQLKTKLP ENLSSKVKLL QLYSEASVAL LK LNNPKDF QELNKQTKKN MTIDGKELTI SPAYLLWDLS AISQSKQDED ISASRFEDNE ELRYSLRSIE RHAPWVRNIF IVT NGQIPS WLNLDNPRVT IVTHQDVFRN LSHLPTFSSP AIESHIHRIE GLSQKFIYLN DDVMFGKDVW PDDFYSHSKG QKVY LTWPV PNCAEGCPGS WIKDGYCDKA CNNSACDWDG GDCSGNSGGS RYIAGGGGTG SIGVGQPWQF GGGINSVSYC NQGCA NSWL ADKFCDQACN VLSCGFDAGD CGQDHFHELY KVILLPNQTH YIIPKGECLP YFSFAEVAKR GVEGAYSDNP IIRHAS IAN KWKTIHLIMH SGMNATTIHF NLTFQNTNDE EFKMQITVEV DTREGPKLNS TAQKGYENLV SPITLLPEAE ILFEDIP KE KRFPKFKRHD VNSTRRAQEE VKIPLVNISL LPKDAQLSLN TLDLQLEHGD ITLKGYNLSK SALLRSFLMN SQHAKIKN Q AIITDETNDS LVAPQEKQVH KSILPNSLGV SERLQRLTFP AVSVKVNGHD QGQNPPLDLE TTARFRVETH TQKTIGGNV TKEKPPSLIV PLESQMTKEK KITGKEKENS RMEENAENHI GVTEVLLGRK LQHYTDSYLG FLPWEKKKYF QDLLDEEESL KTQLAYFTD SKNRARYKRD TFADSLRYVN KILNSKFGFT SRKVPAHMPH MIDRIVMQEL QDMFPEEFDK TSFHKVRHSE D MQFAFSYF YYLMSAVQPL NISQVFDEVD TDQSGVLSDR EIRTLATRIH ELPLSLQDLT GLEHMLINCS KMLPADITQL NN IPPTQES YYDPNLPPVT KSLVTNCKPV TDKIHKAYKD KNKYRFEIMG EEEIAFKMIR TNVSHVVGQL DDIRKNPRKF VCL NDNIDH NHKDAQTVKA VLRDFYESMF PIPSQFELPR EYRNRFLHMH ELQEWRAYRD KLK |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL | ||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 299 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 193.0 K / Max: 193.0 K |
Alignment procedure | Coma free - Residual tilt: 0.05 mrad |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 13320 / Average exposure time: 1.5 sec. / Average electron dose: 66.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |