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Yorodumi- EMDB-13794: Cryo-EM of the complex between human uromodulin (UMOD)/Tamm-Horsf... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13794 | |||||||||||||||
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Title | Cryo-EM of the complex between human uromodulin (UMOD)/Tamm-Horsfall protein (THP) and the FimH lectin domain from uropathogenic E. coli | |||||||||||||||
Map data | Unprocessed cryo-EM map of the lectin domain of fimbrial adhesin FimH from uropathogenic Escherichia coli bound to the branch of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP). | |||||||||||||||
Sample |
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Function / homology | Function and homology information citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / urea transmembrane transport / protein transport into plasma membrane raft / Asparagine N-linked glycosylation / micturition / organ or tissue specific immune response / metanephric ascending thin limb development ...citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / urea transmembrane transport / protein transport into plasma membrane raft / Asparagine N-linked glycosylation / micturition / organ or tissue specific immune response / metanephric ascending thin limb development / urate transport / collecting duct development / renal urate salt excretion / regulation of protein transport / protein localization to vacuole / antibacterial innate immune response / intracellular chloride ion homeostasis / renal sodium ion absorption / juxtaglomerular apparatus development / glomerular filtration / intracellular phosphate ion homeostasis / neutrophil migration / response to water deprivation / potassium ion homeostasis / cell adhesion involved in single-species biofilm formation / intracellular sodium ion homeostasis / regulation of urine volume / endoplasmic reticulum organization / renal water homeostasis / IgG binding / pilus / ciliary membrane / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / extrinsic component of membrane / cellular response to unfolded protein / cellular defense response / multicellular organismal response to stress / side of membrane / chaperone-mediated protein folding / ERAD pathway / tumor necrosis factor-mediated signaling pathway / RNA splicing / apoptotic signaling pathway / lipid metabolic process / autophagy / regulation of blood pressure / cilium / spindle pole / intracellular calcium ion homeostasis / Golgi lumen / basolateral plasma membrane / defense response to Gram-negative bacterium / response to lipopolysaccharide / response to xenobiotic stimulus / inflammatory response / apical plasma membrane / negative regulation of cell population proliferation / calcium ion binding / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Escherichia coli (strain UTI89 / UPEC) (bacteria) / Human (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.4 Å | |||||||||||||||
Authors | Jovine L / Xu C / Stsiapanava A / Carroni M / Tunyasuvunakool K / Jumper J / Wu B | |||||||||||||||
Funding support | Singapore, 4 items
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Citation | Journal: Nature / Year: 2021 Title: Highly accurate protein structure prediction with AlphaFold. Authors: John Jumper / Richard Evans / Alexander Pritzel / Tim Green / Michael Figurnov / Olaf Ronneberger / Kathryn Tunyasuvunakool / Russ Bates / Augustin Žídek / Anna Potapenko / Alex Bridgland ...Authors: John Jumper / Richard Evans / Alexander Pritzel / Tim Green / Michael Figurnov / Olaf Ronneberger / Kathryn Tunyasuvunakool / Russ Bates / Augustin Žídek / Anna Potapenko / Alex Bridgland / Clemens Meyer / Simon A A Kohl / Andrew J Ballard / Andrew Cowie / Bernardino Romera-Paredes / Stanislav Nikolov / Rishub Jain / Jonas Adler / Trevor Back / Stig Petersen / David Reiman / Ellen Clancy / Michal Zielinski / Martin Steinegger / Michalina Pacholska / Tamas Berghammer / Sebastian Bodenstein / David Silver / Oriol Vinyals / Andrew W Senior / Koray Kavukcuoglu / Pushmeet Kohli / Demis Hassabis / Abstract: Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort, the structures of around ...Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort, the structures of around 100,000 unique proteins have been determined, but this represents a small fraction of the billions of known protein sequences. Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence-the structure prediction component of the 'protein folding problem'-has been an important open research problem for more than 50 years. Despite recent progress, existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14), demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13794.map.gz | 193.4 MB | EMDB map data format | |
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Header (meta data) | emd-13794-v30.xml emd-13794.xml | 40.9 KB 40.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13794_fsc.xml | 18.2 KB | Display | FSC data file |
Images | emd_13794.png | 44.5 KB | ||
Others | emd_13794_additional_1.map.gz emd_13794_half_map_1.map.gz emd_13794_half_map_2.map.gz | 54.8 MB 195.1 MB 194.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13794 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13794 | HTTPS FTP |
-Validation report
Summary document | emd_13794_validation.pdf.gz | 395.4 KB | Display | EMDB validaton report |
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Full document | emd_13794_full_validation.pdf.gz | 395 KB | Display | |
Data in XML | emd_13794_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | emd_13794_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13794 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13794 | HTTPS FTP |
-Related structure data
Related structure data | 7q3nMC 7p6rC 7p6sC 7p6tC 7pfpC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13794.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unprocessed cryo-EM map of the lectin domain of fimbrial adhesin FimH from uropathogenic Escherichia coli bound to the branch of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Bound FimH lectin domain density merged with UMOD branch density.
File | emd_13794_additional_1.map | ||||||||||||
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Annotation | Bound FimH lectin domain density merged with UMOD branch density. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map 2 of the lectin domain...
File | emd_13794_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM half map 2 of the lectin domain of fimbrial adhesin FimH from uropathogenic Escherichia coli bound to the branch of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map 1 of the lectin domain...
File | emd_13794_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM half map 1 of the lectin domain of fimbrial adhesin FimH from uropathogenic Escherichia coli bound to the branch of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of human uromodulin (UMOD)/Tamm-Horsfall protein (THP) an...
Entire | Name: Complex of human uromodulin (UMOD)/Tamm-Horsfall protein (THP) and the lectin domain of the FimH adhesin of uropathogenic E. coli |
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Components |
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-Supramolecule #1: Complex of human uromodulin (UMOD)/Tamm-Horsfall protein (THP) an...
Supramolecule | Name: Complex of human uromodulin (UMOD)/Tamm-Horsfall protein (THP) and the lectin domain of the FimH adhesin of uropathogenic E. coli type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Uromodulin
Supramolecule | Name: Uromodulin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Type 1 fimbiral adhesin FimH
Supramolecule | Name: Type 1 fimbiral adhesin FimH / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Escherichia coli (strain UTI89 / UPEC) (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Uromodulin
Macromolecule | Name: Uromodulin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human (human) |
Molecular weight | Theoretical: 61.498816 KDa |
Sequence | String: DTSEARWCSE CHSNATCTED EAVTTCTCQE GFTGDGLTCV DLDECAIPGA HNCSANSSCV NTPGSFSCVC PEGFRLSPGL GCTDVDECA EPGLSHCHAL ATCVNVVGSY LCVCPAGYRG DGWHCECSPG SCGPGLDCVP EGDALVCADP CQAHRTLDEY W RSTEYGEG ...String: DTSEARWCSE CHSNATCTED EAVTTCTCQE GFTGDGLTCV DLDECAIPGA HNCSANSSCV NTPGSFSCVC PEGFRLSPGL GCTDVDECA EPGLSHCHAL ATCVNVVGSY LCVCPAGYRG DGWHCECSPG SCGPGLDCVP EGDALVCADP CQAHRTLDEY W RSTEYGEG YACDTDLRGW YRFVGQGGAR MAETCVPVLR CNTAAPMWLN GTHPSSDEGI VSRKACAHWS GHCCLWDASV QV KACAGGY YVYNLTAPPE CHLAYCTDPS SVEGTCEECS IDEDCKSNNG RWHCQCKQDF NITDISLLEH RLECGANDMK VSL GKCQLK SLGFDKVFMY LSDSRCSGFN DRDNRDWVSV VTPARDGPCG TVLTRNETHA TYSNTLYLAD EIIIRDLNIK INFA CSYPL DMKVSLKTAL QPMVSALNIR VGGTGMFTVR MALFQTPSYT QPYQGSSVTL STEAFLYVGT MLDGGDLSRF ALLMT NCYA TPSSNATDPL KYFIIQDRCP HTRDSTIQVV ENGESSQGRF SVQMFRFAGN YDLVYLHCEV YLCDTMNEKC KPTCSG TRF |
-Macromolecule #2: Type 1 fimbiral adhesin FimH
Macromolecule | Name: Type 1 fimbiral adhesin FimH / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain UTI89 / UPEC) (bacteria) |
Molecular weight | Theoretical: 18.669688 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: FACKTANGTA IPIGGGSANV YVNLAPVVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GAAYGGVLSS FSGTVKYNGS SYPFPTTSE TPRVVYNSRT DKPWPVALYL TPVSSAGGVA IKAGSLIAVL ILRQTNNYNS DDFQFVWNIY ANNDVVVPTG S HHWGHHHH HHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1.8 mg/mL |
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Buffer | pH: 7 / Component - Concentration: 10.0 mM / Component - Formula: C8H17N2NaO4S / Component - Name: Na-HEPES |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 13616 / Average exposure time: 1.7 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
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
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 396.23 | ||||||||
Output model | PDB-7q3n: |