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- EMDB-10553: Cryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (... -

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Entry
Database: EMDB / ID: EMD-10553
TitleCryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
Map dataDensity-modified cryo-em map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament core (estimated resolution 3.35 A).
Sample
  • Complex: Uromodulin (UMOD)/Tamm-Horsfall protein (THP)
    • Protein or peptide: Uromodulin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsZP MODULE / ZP DOMAIN / ZP-N DOMAIN / ZP-C DOMAIN / INTERDOMAIN LINKER / EGF DOMAIN / EXTRACELLULAR MATRIX / GLYCOPROTEIN / N-GLYCAN / STRUCTURAL PROTEIN / PROTEIN FILAMENT / PROTEIN POLYMERIZATION
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 / organ or tissue specific immune response / Asparagine N-linked glycosylation / collecting duct development / metanephric ascending thin limb development / micturition ...citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / protein transport into plasma membrane raft / organ or tissue specific immune response / Asparagine N-linked glycosylation / collecting duct development / metanephric ascending thin limb development / micturition / urea transmembrane transport / protein localization to vacuole / regulation of protein transport / juxtaglomerular apparatus development / antibacterial innate immune response / intracellular chloride ion homeostasis / renal urate salt excretion / glomerular filtration / urate transport / renal sodium ion absorption / neutrophil migration / intracellular phosphate ion homeostasis / response to water deprivation / potassium ion homeostasis / regulation of urine volume / intracellular sodium ion homeostasis / endoplasmic reticulum organization / IgG binding / heterophilic cell-cell adhesion / extrinsic component of membrane / ciliary membrane / leukocyte cell-cell adhesion / cellular response to unfolded protein / cellular defense response / multicellular organismal response to stress / renal water homeostasis / side of membrane / : / ERAD pathway / RNA splicing / tumor necrosis factor-mediated signaling pathway / apoptotic signaling pathway / lipid metabolic process / Golgi lumen / autophagy / regulation of blood pressure / intracellular calcium ion homeostasis / spindle pole / response to lipopolysaccharide / defense response to Gram-negative bacterium / basolateral plasma membrane / cilium / apical plasma membrane / response to xenobiotic stimulus / inflammatory response / 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 / : / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain ...Uromodulin-like, D8C domain / EGF domain / EGF domain / : / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C 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)
Methodhelical reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsStsiapanava A / Xu C
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-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tqk
  • Surface level: 1.8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tqk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10553.png

Downloads & links

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Map

FileDownload / File: emd_10553.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity-modified cryo-em map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament core (estimated resolution 3.35 A).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 93 pix.
= 98.58 Å		1.06 Å/pix.
x 103 pix.
= 109.18 Å		1.06 Å/pix.
x 213 pix.
= 225.78 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: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8 / Movie #1: 1.8
Minimum - Maximum-28.094010999999998 - 45.33775
Average (Standard dev.)0.00000000003902 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin74079
Dimensions10321393
Spacing93103213
CellA: 98.579994 Å / B: 109.17999 Å / C: 225.77998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z93103213
origin x/y/z0.0000.0000.000
length x/y/z98.580109.180225.780
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S321
start NC/NR/NS07479
NC/NR/NS21310393
D min/max/mean-28.09445.3380.000

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Supplemental data

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Additional map: Density-modified cryo-em map of native uromodulin (UMOD)/Tamm-Horsfall protein...

Fileemd_10553_additional_1.map
AnnotationDensity-modified cryo-em map of native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament (estimated resolution 3.76 A).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_10553_additional_2.map
AnnotationUnsharpened cryo-EM map of native 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 native uromodulin (UMOD)/Tamm-Horsfall...

Fileemd_10553_half_map_1.map
AnnotationUnsharpened cryo-EM half map of native 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 native uromodulin (UMOD)/Tamm-Horsfall...

Fileemd_10553_half_map_2.map
AnnotationUnsharpened cryo-EM half map of native 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
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: 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 #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / 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

Concentration0.85 mg/mL
BufferpH: 7
GridModel: Quantifoil R2/2 / Material: GOLD / 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

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: 2300 / Average exposure time: 6.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.4000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000
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: 62.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 180 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: OTHER
Software:
Namedetails
RELION (ver. 3.0.5)
PHENIXphenix.resolve_cryo_em

Details: PHENIX ResolveCryoEM FSCref=0.5 / Number images used: 288403
Segment selectionNumber selected: 412322
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

4wrn

chain_id: A, residue_range: 296-429, source_name: PDB, initial_model_type: experimental model

4wrn

chain_id: A, residue_range: 466-587, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 115.88
Output model

PDB-6tqk:
Cryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament.

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