[English] 日本語
![](img/lk-miru.gif)
- EMDB-40594: Xenopus laevis hyaluronan synthase 1, nascent HA polymer bound state -
+
Open data
-
Basic information
Entry | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Xenopus laevis hyaluronan synthase 1, nascent HA polymer bound state | ||||||||||||
![]() | Xenopus laevis hyaluronan synthase 1, nascent HA polymer bound state | ||||||||||||
![]() |
| ||||||||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Gorniak I / Zimmer J | ||||||||||||
Funding support | ![]() ![]()
| ||||||||||||
![]() | ![]() Title: Atomistic insights into hyaluronan synthesis, secretion, and length control Authors: Gorniak I / Stephens ZS / Erramilli SK / Gawda T / Kossiakoff AA / Zimmer J | ||||||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 118 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 22.3 KB 22.3 KB | Display Display | ![]() |
Images | ![]() | 32.7 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() ![]() | 117.6 MB 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8smnMC ![]() 8smmC ![]() 8smpC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Xenopus laevis hyaluronan synthase 1, nascent HA polymer bound state | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Additional Map
File | emd_40594_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Additional Map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map A
File | emd_40594_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map B
File | emd_40594_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecu...
Entire | Name: Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecule, nascent HA polymer bound state |
---|---|
Components |
|
-Supramolecule #1: Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecu...
Supramolecule | Name: Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecule, nascent HA polymer bound state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 118 KDa |
-Macromolecule #1: Hyaluronan synthase 1
Macromolecule | Name: Hyaluronan synthase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ![]() |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 70.385047 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MHHHHHHHHH HHHMKEKAAE TMEIPEGIPK DLEPKHPTLW RIIYYSFGVV LLATITAAYV AEFQVLKHEA ILFSLGLYGL AMLLHLMMQ SLFAFLEIRR VNKSELPCSF KKTVALTIAG YQENPEYLIK CLESCKYVKY PKDKLKIILV IDGNTEDDAY M MEMFKDVF ...String: MHHHHHHHHH HHHMKEKAAE TMEIPEGIPK DLEPKHPTLW RIIYYSFGVV LLATITAAYV AEFQVLKHEA ILFSLGLYGL AMLLHLMMQ SLFAFLEIRR VNKSELPCSF KKTVALTIAG YQENPEYLIK CLESCKYVKY PKDKLKIILV IDGNTEDDAY M MEMFKDVF HGEDVGTYVW KGNYHTVKKP EETNKGSCPE VSKPLNEDEG INMVEELVRN KRCVCIMQQW GGKREVMYTA FQ AIGTSVD YVQVCDSDTK LDELATVEMV KVLESNDMYG AVGGDVRILN PYDSFISFMS SLRYWMAFNV ERACQSYFDC VSC ISGPLG MYRNNILQVF LEAWYRQKFL GTYCTLGDDR HLTNRVLSMG YRTKYTHKSR AFSETPSLYL RWLNQQTRWT KSYF REWLY NAQWWHKHHI WMTYESVVSF IFPFFITATV IRLIYAGTIW NVVWLLLCIQ IMSLFKSIYA CWLRGNFIML LMSLY SMLY MTGLLPSKYF ALLTLNKTGW GTSGRKKIVG NYMPILPLSI WAAVLCGGVG YSIYMDCQND WSTPEKQKEM YHLLYG CVG YVMYWVIMAV MYWVWVKRCC RKRSQTVTLV HDIPDMCV UniProtKB: ![]() |
-Macromolecule #2: Fab15 heavy chain
Macromolecule | Name: Fab15 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.674379 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSYYIHWV RQAPGKGLEW VASISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSGYYWGPY FGGFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSYYIHWV RQAPGKGLEW VASISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSGYYWGPY FGGFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKTHT |
-Macromolecule #3: Fab15 light chain
Macromolecule | Name: Fab15 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.258783 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 1 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Concentration | 8 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.8 Component:
| ||||||||||||
Grid | Model: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Particle selection | Number selected: 11732347 |
---|---|
Startup model | Type of model: NONE |
Initial angle assignment | Type: NOT APPLICABLE / Software - Name: cryoSPARC |
Final 3D classification | Number classes: 4 / Software - Name: cryoSPARC |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: cryoSPARC |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 171641 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
---|---|
Output model | ![]() PDB-8smn: |