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- EMDB-25037: Cryo-EM 3D map of the human Exostosin-1 and Exostosin-2 heterodim... -
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Open data
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Basic information
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Title | Cryo-EM 3D map of the human Exostosin-1 and Exostosin-2 heterodimer in complex with a 7-sugar oligosaccharide acceptor analog | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Li H | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 56.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.9 KB 21.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 162.6 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() ![]() | 6.4 MB 49.7 MB 49.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sckMC ![]() 7schC ![]() 7scjC ![]() 7uqxC ![]() 7uqyC 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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Related items in Molecule of the Month |
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Map
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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
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_25037_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_25037_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_25037_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : human EXT1/2
Entire | Name: human EXT1/2 |
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Components |
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-Supramolecule #1: human EXT1/2
Supramolecule | Name: human EXT1/2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Exostosin-1
Macromolecule | Name: Exostosin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 83.404023 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 77.238031 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GWPHSIESSN DWNVEKRSIR DVPVVRLPAD SPIPERGDLS CRMHTCFDVY RCGFNPKNKI KVYIYALKKY VDDFGVSVSN TISREYNEL LMAISDSDYY TDDINRACLF VPSIDVLNQN TLRIKETAQA MAQLSRWDRG TNHLLFNMLP GGPPDYNTAL D VPRDRALL ...String: GWPHSIESSN DWNVEKRSIR DVPVVRLPAD SPIPERGDLS CRMHTCFDVY RCGFNPKNKI KVYIYALKKY VDDFGVSVSN TISREYNEL LMAISDSDYY TDDINRACLF VPSIDVLNQN TLRIKETAQA MAQLSRWDRG TNHLLFNMLP GGPPDYNTAL D VPRDRALL AGGGFSTWTY RQGYDVSIPV YSPLSAEVDL PEKGPGPRQY FLLSSQVGLH PEYREDLEAL QVKHGESVLV LD KCTNLSE GVLSVRKRCH KHQVFDYPQV LQEATFCVVL RGARLGQAVL SDVLQAGCVP VVIADSYILP FSEVLDWKRA SVV VPEEKM SDVYSILQSI PQRQIEEMQR QARWFWEAYF QSIKAIALAT LQIINDRIYP YAAISYEEWN DPPAVKWGSV SNPL FLPLI PPQSQGFTAI VLTYDRVESL FRVITEVSKV PSLSKLLVVW NNQNKNPPED SLWPKIRVPL KVVRTAENKL SNRFF PYDE IETEAVLAID DDIIMLTSDE LQFGYEVWRE FPDRLVGYPG RLHLWDHEMN KWKYESEWTN EVSMVLTGAA FYHKYF NYL YTYKMPGDIK NWVDAHMNCE DIAMNFLVAN VTGKAVIKVT PRKKFKCPEC TAIDGLSLDQ THMVERSECI NKFASVF GT MPLKVVEHRA DPVLYKDDFP EKLKSFPNIG SL |
-Macromolecule #5: URIDINE-5'-DIPHOSPHATE
Macromolecule | Name: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: UDP |
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Molecular weight | Theoretical: 404.161 Da |
Chemical component information | ![]() ChemComp-UDP: |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 1 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #7: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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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 | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 299 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
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 | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 5108 / #0 - Average exposure time: 1.5 sec. / #0 - Average electron dose: 68.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Digitization - Dimensions - Width: 5760 pixel / #1 - Digitization - Dimensions - Height: 4092 pixel / #1 - Number grids imaged: 1 / #1 - Number real images: 7609 / #1 - Average exposure time: 1.5 sec. / #1 - Average electron dose: 72.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7sck: |