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Yorodumi- EMDB-25036: Cryo-EM 3D map of the human Exostosin-1 and Exostosin-2 heterodim... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25036 | |||||||||
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Title | Cryo-EM 3D map of the human Exostosin-1 and Exostosin-2 heterodimer in complex with a 4-sugar oligosaccharide acceptor analog | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase / hypersensitivity / heart field specification / lymphocyte adhesion to endothelial cell of high endothelial venule / heparan sulfate N-acetylglucosaminyltransferase activity / glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity / smoothened signaling pathway involved in lung development / developmental growth involved in morphogenesis ...glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase / hypersensitivity / heart field specification / lymphocyte adhesion to endothelial cell of high endothelial venule / heparan sulfate N-acetylglucosaminyltransferase activity / glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity / smoothened signaling pathway involved in lung development / developmental growth involved in morphogenesis / sweat gland development / perichondral bone morphogenesis / mesenchymal cell differentiation involved in bone development / response to leukemia inhibitory factor / UDP-N-acetylglucosamine transferase complex / chondroitin sulfate metabolic process / response to heparin / chondrocyte hypertrophy / embryonic skeletal joint development / hematopoietic stem cell migration to bone marrow / heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process / fluid transport / glucuronosyltransferase activity / limb joint morphogenesis / tight junction organization / heparin biosynthetic process / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / endochondral bone growth / stomach development / sebaceous gland development / glomerular basement membrane development / heparan sulfate proteoglycan biosynthetic process / dendrite self-avoidance / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process / lymphocyte migration into lymphoid organs / chondrocyte proliferation / hematopoietic stem cell homeostasis / sulfation / dendritic cell migration / endochondral bone morphogenesis / glandular epithelial cell differentiation / acetylglucosaminyltransferase activity / sodium ion homeostasis / podocyte differentiation / basement membrane organization / polysaccharide biosynthetic process / cartilage development involved in endochondral bone morphogenesis / vocalization behavior / cranial skeletal system development / fear response / stem cell division / leukocyte tethering or rolling / vacuole organization / multicellular organismal-level water homeostasis / olfactory bulb development / endochondral ossification / endoderm development / response to light intensity / regulation of tumor necrosis factor-mediated signaling pathway / protein N-linked glycosylation / cellular response to fibroblast growth factor stimulus / collagen fibril organization / neural crest cell differentiation / motor behavior / ossification involved in bone maturation / hair follicle morphogenesis / cell adhesion mediated by integrin / optic nerve development / epithelial tube branching involved in lung morphogenesis / heart contraction / glycosyltransferase activity / mesoderm development / protein glycosylation / antigen processing and presentation / social behavior / mesoderm formation / catalytic complex / blood vessel remodeling / cell fate commitment / fibroblast growth factor receptor signaling pathway / hematopoietic stem cell differentiation / canonical Wnt signaling pathway / chondrocyte differentiation / BMP signaling pathway / bone resorption / gastrulation / ossification / axon guidance / synaptic transmission, glutamatergic / wound healing / protein catabolic process / multicellular organism growth / cellular response to virus / regulation of blood pressure / vasodilation / gene expression / protein-containing complex assembly / protein heterodimerization activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Li H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Chem Biol / Year: 2023 Title: Structural basis for heparan sulfate co-polymerase action by the EXT1-2 complex. Authors: Hua Li / Digantkumar Chapla / Robert A Amos / Annapoorani Ramiah / Kelley W Moremen / Huilin Li / Abstract: Heparan sulfate (HS) proteoglycans are extended (-GlcAβ1,4GlcNAcα1,4-) co-polymers containing decorations of sulfation and epimerization that are linked to cell surface and extracellular matrix ...Heparan sulfate (HS) proteoglycans are extended (-GlcAβ1,4GlcNAcα1,4-) co-polymers containing decorations of sulfation and epimerization that are linked to cell surface and extracellular matrix proteins. In mammals, HS repeat units are extended by an obligate heterocomplex of two exostosin family members, EXT1 and EXT2, where each protein monomer contains distinct GT47 (GT-B fold) and GT64 (GT-A fold) glycosyltransferase domains. In this study, we generated human EXT1-EXT2 (EXT1-2) as a functional heterocomplex and determined its structure in the presence of bound donor and acceptor substrates. Structural data and enzyme activity of catalytic site mutants demonstrate that only two of the four glycosyltransferase domains are major contributors to co-polymer syntheses: the EXT1 GT-B fold β1,4GlcA transferase domain and the EXT2 GT-A fold α1,4GlcNAc transferase domain. The two catalytic sites are over 90 Å apart, indicating that HS is synthesized by a dissociative process that involves a single catalytic site on each monomer. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25036.map.gz | 56.8 MB | EMDB map data format | |
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Header (meta data) | emd-25036-v30.xml emd-25036.xml | 21.1 KB 21.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25036_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_25036.png | 158.9 KB | ||
Masks | emd_25036_msk_1.map | 64 MB | Mask map | |
Others | emd_25036_additional_1.map.gz emd_25036_half_map_1.map.gz emd_25036_half_map_2.map.gz | 5.8 MB 49.6 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25036 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25036 | HTTPS FTP |
-Validation report
Summary document | emd_25036_validation.pdf.gz | 749.3 KB | Display | EMDB validaton report |
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Full document | emd_25036_full_validation.pdf.gz | 748.8 KB | Display | |
Data in XML | emd_25036_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_25036_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25036 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25036 | HTTPS FTP |
-Related structure data
Related structure data | 7scjMC 7schC 7sckC 7uqxC 7uqyC 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_25036.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Mask #1
File | emd_25036_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_25036_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_25036_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_25036_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : hEXT1/2
Entire | Name: hEXT1/2 |
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Components |
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-Supramolecule #1: hEXT1/2
Supramolecule | Name: hEXT1/2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Exostosin-1
Macromolecule | Name: Exostosin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 83.404023 KDa |
Recombinant expression | Organism: Mammalia (mammals) |
Sequence | String: GFRASRSHSR REEHSGRNGL HHPSPDHFWP RFPDALRPFV PWDQLENEDS SVHISPRQKR DANSSIYKGK KCRMESCFDF TLCKKNGFK VYVYPQQKGE KIAESYQNIL AAIEGSRFYT SDPSQACLFV LSLDTLDRDQ LSPQYVHNLR SKVQSLHLWN N GRNHLIFN ...String: GFRASRSHSR REEHSGRNGL HHPSPDHFWP RFPDALRPFV PWDQLENEDS SVHISPRQKR DANSSIYKGK KCRMESCFDF TLCKKNGFK VYVYPQQKGE KIAESYQNIL AAIEGSRFYT SDPSQACLFV LSLDTLDRDQ LSPQYVHNLR SKVQSLHLWN N GRNHLIFN LYSGTWPDYT EDVGFDIGQA MLAKASISTE NFRPNFDVSI PLFSKDHPRT GGERGFLKFN TIPPLRKYML VF KGKRYLT GIGSDTRNAL YHVHNGEDVV LLTTCKHGKD WQKHKDSRCD RDNTEYEKYD YREMLHNATF CLVPRGRRLG SFR FLEALQ AACVPVMLSN GWELPFSEVI NWNQAAVIGD ERLLLQIPST IRSIHQDKIL ALRQQTQFLW EAYFSSVEKI VLTT LEIIQ DRIFKHISRN SLIWNKHPGG LFVLPQYSSY LGDFPYYYAN LGLKPPSKFT AVIHAVTPLV SQSQPVLKLL VAAAK SQYC AQIIVLWNCD KPLPAKHRWP ATAVPVVVIE GESKVMSSRF LPYDNIITDA VLSLDEDTVL STTEVDFAFT VWQSFP ERI VGYPARSHFW DNSKERWGYT SKWTNDYSMV LTGAAIYHKY YHYLYSHYLP ASLKNMVDQL ANCEDILMNF LVSAVTK LP PIKVTQKKQY KETMMGQTSR ASRWADPDHF AQRQSCMNTF ASWFGYMPLI HSQMRLDPVL FKDQVSILRK KYRDIERL |
-Macromolecule #2: Exostosin-2
Macromolecule | Name: Exostosin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 77.180984 KDa |
Recombinant expression | Organism: Mammalia (mammals) |
Sequence | String: WPHSIESSND WNVEKRSIRD VPVVRLPADS PIPERGDLSC RMHTCFDVYR CGFNPKNKIK VYIYALKKYV DDFGVSVSNT ISREYNELL MAISDSDYYT DDINRACLFV PSIDVLNQNT LRIKETAQAM AQLSRWDRGT NHLLFNMLPG GPPDYNTALD V PRDRALLA ...String: WPHSIESSND WNVEKRSIRD VPVVRLPADS PIPERGDLSC RMHTCFDVYR CGFNPKNKIK VYIYALKKYV DDFGVSVSNT ISREYNELL MAISDSDYYT DDINRACLFV PSIDVLNQNT LRIKETAQAM AQLSRWDRGT NHLLFNMLPG GPPDYNTALD V PRDRALLA GGGFSTWTYR QGYDVSIPVY SPLSAEVDLP EKGPGPRQYF LLSSQVGLHP EYREDLEALQ VKHGESVLVL DK CTNLSEG VLSVRKRCHK HQVFDYPQVL QEATFCVVLR GARLGQAVLS DVLQAGCVPV VIADSYILPF SEVLDWKRAS VVV PEEKMS DVYSILQSIP QRQIEEMQRQ ARWFWEAYFQ SIKAIALATL QIINDRIYPY AAISYEEWND PPAVKWGSVS NPLF LPLIP PQSQGFTAIV LTYDRVESLF RVITEVSKVP SLSKLLVVWN NQNKNPPEDS LWPKIRVPLK VVRTAENKLS NRFFP YDEI ETEAVLAIDD DIIMLTSDEL QFGYEVWREF PDRLVGYPGR LHLWDHEMNK WKYESEWTNE VSMVLTGAAF YHKYFN YLY TYKMPGDIKN WVDAHMNCED IAMNFLVANV TGKAVIKVTP RKKFKCPECT AIDGLSLDQT HMVERSECIN KFASVFG TM PLKVVEHRAD PVLYKDDFPE KLKSFPNIGS L |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #6: URIDINE-5'-DIPHOSPHATE
Macromolecule | Name: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: UDP |
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Molecular weight | Theoretical: 404.161 Da |
Chemical component information | ChemComp-UDP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | |||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | |||||||||
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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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: 3080 / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2 |
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 FIELD / Cs: 2.7 mm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7scj: |