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- EMDB-10554: Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall... -

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Basic information

Entry
Database: EMDB / ID: EMD-10554
TitleCryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
Map dataDensity-modified cryo-EM map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament (estimated resolution 3.96 A).
Sample
  • Complex: Uromodulin (UMOD)/Tamm-Horsfall protein (THP)
    • Protein or peptide: Uromodulin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / urea transmembrane transport / micturition / 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 / urea transmembrane transport / micturition / metanephric ascending thin limb development / collecting duct development / regulation of protein transport / protein localization to vacuole / urate transport / renal urate salt excretion / intracellular chloride ion homeostasis / antibacterial innate immune response / juxtaglomerular apparatus development / renal sodium ion absorption / glomerular filtration / intracellular phosphate ion homeostasis / neutrophil migration / response to water deprivation / potassium ion homeostasis / intracellular sodium ion homeostasis / regulation of urine volume / endoplasmic reticulum organization / IgG binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / ciliary membrane / extrinsic component of membrane / leukocyte cell-cell adhesion / cellular response to unfolded protein / multicellular organismal response to stress / renal water homeostasis / cellular defense response / side of membrane / chaperone-mediated protein folding / ERAD pathway / tumor necrosis factor-mediated signaling pathway / RNA splicing / apoptotic signaling pathway / lipid metabolic process / cilium / regulation of blood pressure / autophagy / spindle pole / Golgi lumen / intracellular calcium ion homeostasis / basolateral plasma membrane / defense response to Gram-negative bacterium / response to lipopolysaccharide / inflammatory response / response to xenobiotic stimulus / apical plasma membrane / negative regulation of cell population proliferation / calcium ion binding / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / membrane
Similarity search - Function
EGF domain / : / EGF domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain ...EGF domain / : / EGF domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / : / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Human (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsStsiapanava A / Xu C / Carroni M / Wu B / Jovine L
Funding support Sweden, Singapore, 4 items
OrganizationGrant numberCountry
Swedish Research Council2016-03999 Sweden
Knut and Alice Wallenberg Foundation2018.0042 Sweden
Ministry of Education (MoE, Singapore)2017-T1-001-168 Singapore
Ministry of Education (MoE, Singapore)2016-T2-1-010 Singapore
Citation
Journal: Curr Top Dev Biol / Year: 2018
Title: Structure of Zona Pellucida Module Proteins.
Authors: Marcel Bokhove / Luca Jovine /
Abstract: The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common ...The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common zona pellucida (ZP) "domain" module that consists of two related immunoglobulin-like domains, called ZP-N and ZP-C. The ZP module has also been recognized in a large number of other secreted proteins with different biological functions, whose mutations are linked to severe human diseases. During the last decade, tremendous progress has been made toward understanding the atomic architecture of the ZP module and the structural basis of its polymerization. Moreover, sperm-binding regions at the N-terminus of mollusk and mammalian egg coat subunits were found to consist of domain repeats that also adopt a ZP-N fold. This discovery revealed an unexpected link between invertebrate and vertebrate fertilization and led to the first structure of an egg coat-sperm protein recognition complex. In this review we summarize these exciting findings, discuss their functional implications, and outline future challenges that must be addressed in order to develop a comprehensive view of this family of biomedically important extracellular molecules.
#2: Journal: Biol. Cellulaire / Year: 1980
Title: Etude chimique et ultrastructurale de la glycoproteine de Tamm et Horsfall ou uromucoide.
Authors: Delain E / Thiery JP / Coulard D / Joliviene A / Hartman L
#14: Journal: bioRxiv / Year: 2020
Title: Cryo-EM structure of native human uromodulin, a zona pellucida module polymer.
Authors: Stsiapanava A / Xu C / Brunati M / Zamora-Caballero S / Schaeffer C / Han L / Carroni M / Yasumasu S / Rampoldi L / Wu B / Jovine L
History
DepositionDec 16, 2019-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tql
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tql
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10554.png

Downloads & links

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Map

FileDownload / File: emd_10554.map.gz / Format: CCP4 / Size: 15.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity-modified cryo-EM map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament (estimated resolution 3.96 A).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.82 Å/pix.
x 135 pix.
= 110.7 Å		0.82 Å/pix.
x 84 pix.
= 68.88 Å		0.82 Å/pix.
x 349 pix.
= 286.18 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-15.694388 - 20.388788
Average (Standard dev.)1.216708e-11 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin1340108
Dimensions84349135
Spacing13584349
CellA: 110.7 Å / B: 68.88 Å / C: 286.18 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z13584349
origin x/y/z0.0000.0000.000
length x/y/z110.70068.880286.180
α/β/γ90.00090.00090.000
start NX/NY/NZ1081340
NX/NY/NZ13584349
MAP C/R/S321
start NC/NR/NS0134108
NC/NR/NS34984135
D min/max/mean-15.69420.3890.000

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Supplemental data

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Additional map: Unsharpened cryo-EM map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein...

Fileemd_10554_additional_1.map
AnnotationUnsharpened cryo-EM map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 10554 additional 2.map

Fileemd_10554_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened cryo-EM half map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall...

Fileemd_10554_half_map_1.map
AnnotationUnsharpened cryo-EM half map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened cryo-EM half map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall...

Fileemd_10554_half_map_2.map
AnnotationUnsharpened cryo-EM half map of elastase-treated uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Uromodulin (UMOD)/Tamm-Horsfall protein (THP)

EntireName: Uromodulin (UMOD)/Tamm-Horsfall protein (THP)
Components
  • Complex: Uromodulin (UMOD)/Tamm-Horsfall protein (THP)
    • Protein or peptide: Uromodulin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Uromodulin (UMOD)/Tamm-Horsfall protein (THP)

SupramoleculeName: Uromodulin (UMOD)/Tamm-Horsfall protein (THP) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Elastase-resistant fragment
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Uromodulin

MacromoleculeName: Uromodulin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 33.211594 KDa
SequenceString: SVEGTCEECS IDEDCKSNNG RWHCQCKQDF NITDISLLEH RLECGANDMK VSLGKCQLKS LGFDKVFMYL SDSRCSGFND RDNRDWVSV VTPARDGPCG TVLTRNETHA TYSNTLYLAD EIIIRDLNIK INFACSYPLD MKVSLKTALQ PMVSALNIRV G GTGMFTVR ...String:
SVEGTCEECS IDEDCKSNNG RWHCQCKQDF NITDISLLEH RLECGANDMK VSLGKCQLKS LGFDKVFMYL SDSRCSGFND RDNRDWVSV VTPARDGPCG TVLTRNETHA TYSNTLYLAD EIIIRDLNIK INFACSYPLD MKVSLKTALQ PMVSALNIRV G GTGMFTVR MALFQTPSYT QPYQGSSVTL STEAFLYVGT MLDGGDLSRF ALLMTNCYAT PSSNATDPLK YFIIQDRCPH TR DSTIQVV ENGESSQGRF SVQMFRFAGN YDLVYLHCEV YLCDTMNEKC KPTCSGTRF

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.00 mg/mL
BufferpH: 7 / Component - Concentration: 10.0 mM / Component - Formula: C8H17N2NaO4S / Component - Name: Na-HEPES
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV
DetailsObtained by limited proteolysis of purified native human uromodulin filaments with porcine pancreatic elastase.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5683 / Average exposure time: 6.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.4000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000
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

Final reconstructionApplied symmetry - Helical parameters - Δz: 62.7 Å
Applied symmetry - Helical parameters - Δ&Phi: -179.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: OTHER
Software:
Namedetails
RELION (ver. 3.0.5)
PHENIXphenix.resolve_cryo_em

Details: PHENIX ResolveCryoEM FSCref=0.5 / Number images used: 94937
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Segment selectionNumber selected: 252438 / Software - Name: RELION (ver. 3.0.5)
Startup modelType of model: OTHER / Details: Featureless Gaussian cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6tqk

chain_id: A

6tqk

chain_id: B

6tqk

chain_id: C
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 171
Output model

PDB-6tql:
Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament

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