- EMDB-13794: Cryo-EM of the complex between human uromodulin (UMOD)/Tamm-Horsf... -
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Basic information
Entry
Database: EMDB / ID: EMD-13794
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
Complex: Complex of human uromodulin (UMOD)/Tamm-Horsfall protein (THP) and the lectin domain of the FimH adhesin of uropathogenic E. coli
Complex: Uromodulin
Protein or peptide: Uromodulin
Complex: Type 1 fimbiral adhesin FimH
Protein or peptide: Type 1 fimbiral adhesin FimH
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 / cilium / regulation of blood pressure / 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
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
Deposition
Oct 28, 2021
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Header (metadata) release
Mar 16, 2022
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Map release
Mar 16, 2022
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Update
Mar 30, 2022
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Current status
Mar 30, 2022
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
#262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1)
#29 - May 2002 Penicillin-binding Proteins similarity (1)
#95 - Nov 2007 Multidrug Resistance Transporters similarity (1)
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Map
File
Download / File: emd_13794.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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).
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).
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).
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
Components
Complex: Complex of human uromodulin (UMOD)/Tamm-Horsfall protein (THP) and the lectin domain of the FimH adhesin of uropathogenic E. coli
Complex: Uromodulin
Protein or peptide: Uromodulin
Complex: Type 1 fimbiral adhesin FimH
Protein or peptide: Type 1 fimbiral adhesin FimH
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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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