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- EMDB-13794: Cryo-EM of the complex between human uromodulin (UMOD)/Tamm-Horsf... -

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Entry
Database: EMDB / ID: EMD-13794
TitleCryo-EM of the complex between human uromodulin (UMOD)/Tamm-Horsfall protein (THP) and the FimH lectin domain from uropathogenic E. coli
Map dataUnprocessed 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
KeywordsEGF DOMAIN / DECOY MODULE / BETA-HAIRPIN / D10C DOMAIN / D8C DOMAIN / EXTRACELLULAR MATRIX / GLYCOPROTEIN / N-GLYCAN / HIGH-MANNOSE SUGAR / CELL ADHESION / ANTIMICROBIAL PROTEIN / BACTERIAL ADHESIN / TYPE I PILUS / SUGAR BINDING PROTEIN / LECTIN / URINARY TRACT INFECTION / UTI / UROPATHOGENIC E. COLI / UPEC
Function / homology
Function and homology information


citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / protein transport into plasma membrane raft / Asparagine N-linked glycosylation / organ or tissue specific immune response / collecting duct development / urea transmembrane transport / metanephric ascending thin limb development ...citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / protein transport into plasma membrane raft / Asparagine N-linked glycosylation / organ or tissue specific immune response / collecting duct development / urea transmembrane transport / metanephric ascending thin limb development / regulation of protein transport / micturition / protein localization to vacuole / intracellular chloride ion homeostasis / juxtaglomerular apparatus development / antibacterial innate immune response / renal urate salt excretion / urate transport / renal sodium ion absorption / glomerular filtration / neutrophil migration / intracellular phosphate ion homeostasis / response to water deprivation / potassium ion homeostasis / intracellular sodium ion homeostasis / regulation of urine volume / endoplasmic reticulum organization / cell adhesion involved in single-species biofilm formation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / IgG binding / pilus / extrinsic component of membrane / ciliary membrane / leukocyte cell-cell adhesion / cellular response to unfolded protein / multicellular organismal response to stress / cellular defense response / renal water homeostasis / side of membrane / tumor necrosis factor-mediated signaling pathway / ERAD pathway / : / RNA splicing / apoptotic signaling pathway / regulation of blood pressure / lipid metabolic process / autophagy / Golgi lumen / intracellular calcium ion homeostasis / spindle pole / defense response to Gram-negative bacterium / basolateral plasma membrane / response to lipopolysaccharide / cilium / apical plasma membrane / inflammatory response / response to xenobiotic stimulus / negative regulation of cell population proliferation / calcium ion binding / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / membrane
Similarity search - Function
Uromodulin-like, D8C domain / EGF domain / EGF domain / : / : / : / ZP-N domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain ...Uromodulin-like, D8C domain / EGF domain / EGF domain / : / : / : / ZP-N domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / : / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Uromodulin / Type 1 fimbiral adhesin FimH
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia coli (strain UTI89 / UPEC) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsJovine L / Xu C
Funding support Singapore, 4 items
OrganizationGrant numberCountry
Swedish Research Council2016-03999 Singapore
Swedish Research Council2020-04936 Singapore
Knut and Alice Wallenberg Foundation2018.0042 Singapore
Ministry of Education (MoE, Singapore)MOH-000382-00 Singapore
CitationJournal: 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
DepositionOct 28, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.001
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.001
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7q3n
  • Surface level: 0.001
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13794.png

Downloads & links

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Map

FileDownload / File: emd_13794.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnprocessed 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

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001 / Movie #1: 0.001
Minimum - Maximum-0.0062941606 - 0.01860563
Average (Standard dev.)0.000026052234 (±0.00019823122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0060.0190.000

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Supplemental data

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Additional map: Bound FimH lectin domain density merged with UMOD branch density.

Fileemd_13794_additional_1.map
AnnotationBound FimH lectin domain density merged with UMOD branch density.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map 2 of the lectin domain...

Fileemd_13794_half_map_1.map
AnnotationCryo-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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map 1 of the lectin domain...

Fileemd_13794_half_map_2.map
AnnotationCryo-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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of human uromodulin (UMOD)/Tamm-Horsfall protein (THP) an...

EntireName: 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...

SupramoleculeName: 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

SupramoleculeName: Uromodulin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Type 1 fimbiral adhesin FimH

SupramoleculeName: Type 1 fimbiral adhesin FimH / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia coli (strain UTI89 / UPEC) (bacteria)

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Macromolecule #1: Uromodulin

MacromoleculeName: Uromodulin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.498816 KDa
SequenceString: 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

UniProtKB: Uromodulin

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Macromolecule #2: Type 1 fimbiral adhesin FimH

MacromoleculeName: Type 1 fimbiral adhesin FimH / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain UTI89 / UPEC) (bacteria)
Molecular weightTheoretical: 18.669688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
FACKTANGTA IPIGGGSANV YVNLAPVVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GAAYGGVLSS FSGTVKYNGS SYPFPTTSE TPRVVYNSRT DKPWPVALYL TPVSSAGGVA IKAGSLIAVL ILRQTNNYNS DDFQFVWNIY ANNDVVVPTG S HHWGHHHH HHHH

UniProtKB: Type 1 fimbiral adhesin FimH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.8 mg/mL
BufferpH: 7 / Component - Concentration: 10.0 mM / Component - Formula: C8H17N2NaO4S / Component - Name: Na-HEPES
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3767790
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6tqk


Details: Cryo-EM structure of the filament core of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP).
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 225819
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.08)
Details: 483997 helical segments were used during final 3D classification.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7pfp

chain_id: C, residue_range: 25-316, source_name: PDB, initial_model_type: experimental model

6gtw

chain_id: A, residue_range: 1-158, source_name: PDB, initial_model_type: experimental model

6gtw

chain_id: F, residue_range: 1-2, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 396.23
Output model

PDB-7q3n:
Cryo-EM of the complex between human uromodulin (UMOD)/Tamm-Horsfall protein (THP) and the FimH lectin domain from uropathogenic E. coli

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