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- EMDB-13378: Full-length cryo-EM structure of the native human uromodulin (UMO... -

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Basic information

Entry
Database: EMDB / ID: EMD-13378
TitleFull-length cryo-EM structure of the native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
Map dataComposite cryo-EM map of the native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament.
Sample
  • Complex: Uromodulin (UMOD)/Tamm-Horsfall protein (THP)
    • Protein or peptide: Uromodulin
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 / intracellular sodium ion homeostasis / regulation of urine volume / endoplasmic reticulum organization / renal water homeostasis / IgG binding / 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
: / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / EGF domain / Zona pellucida-like domain / Zona pellucida (ZP) domain / EGF domain / ZP domain profile. / Zona pellucida domain ...: / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / EGF domain / Zona pellucida-like domain / Zona pellucida (ZP) domain / EGF 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsJovine L / Xu C / Stsiapanava A / Carroni M / Tunyasuvunakool K / Jumper J / Wu B
Funding support Sweden, 4 items
OrganizationGrant numberCountry
Swedish Research Council2016-03999 Sweden
Swedish Research Council2020-04936 Sweden
Knut and Alice Wallenberg Foundation2018.0042 Sweden
Ministry of Education (MoE, Singapore)MOH-000382-00 Sweden
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
DepositionAug 11, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pfp
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pfp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13378.png

Downloads & links

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Map

FileDownload / File: emd_13378.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite cryo-EM map of the native uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament.
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.015885687 - 0.057409693
Average (Standard dev.)0.0007697676 (±0.0031171339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.000212.000212.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0160.0570.001

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Supplemental data

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Additional map: Cryo-EM half map 2 of the branch of...

Fileemd_13378_additional_1.map
AnnotationCryo-EM half map 2 of the branch of the 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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Additional map: Cryo-EM half map 1 of the branch of...

Fileemd_13378_additional_2.map
AnnotationCryo-EM half map 1 of the branch of the 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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Additional map: Unprocessed cryo-EM map of the branch of the...

Fileemd_13378_additional_3.map
AnnotationUnprocessed cryo-EM map of the branch of the 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

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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: all
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: 69.82168 KDa
SequenceString: MGQPSLTWML MVVVASWFIT TAATDTSEAR WCSECHSNAT CTEDEAVTTC TCQEGFTGDG LTCVDLDECA IPGAHNCSAN SSCVNTPGS FSCVCPEGFR LSPGLGCTDV DECAEPGLSH CHALATCVNV VGSYLCVCPA GYRGDGWHCE CSPGSCGPGL D CVPEGDAL ...String:
MGQPSLTWML MVVVASWFIT TAATDTSEAR WCSECHSNAT CTEDEAVTTC TCQEGFTGDG LTCVDLDECA IPGAHNCSAN SSCVNTPGS FSCVCPEGFR LSPGLGCTDV DECAEPGLSH CHALATCVNV VGSYLCVCPA GYRGDGWHCE CSPGSCGPGL D CVPEGDAL VCADPCQAHR TLDEYWRSTE YGEGYACDTD LRGWYRFVGQ GGARMAETCV PVLRCNTAAP MWLNGTHPSS DE GIVSRKA CAHWSGHCCL WDASVQVKAC AGGYYVYNLT APPECHLAYC TDPSSVEGTC EECSIDEDCK SNNGRWHCQC KQD FNITDI SLLEHRLECG ANDMKVSLGK CQLKSLGFDK VFMYLSDSRC SGFNDRDNRD WVSVVTPARD GPCGTVLTRN ETHA TYSNT LYLADEIIIR DLNIKINFAC SYPLDMKVSL KTALQPMVSA LNIRVGGTGM FTVRMALFQT PSYTQPYQGS SVTLS TEAF LYVGTMLDGG DLSRFALLMT NCYATPSSNA TDPLKYFIIQ DRCPHTRDST IQVVENGESS QGRFSVQMFR FAGNYD LVY LHCEVYLCDT MNEKCKPTCS GTRFRSGSVI DQSRVLNLGP ITRKGVQATV SRAFSSLGLL KVWLPLLLSA TLTLTFQ

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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

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 - 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

Particle selectionNumber selected: 412322
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.5) / Number images used: 114206
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6tqk


7p6s

chain_id: A

7p6t

chain_id: A
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7pfp:
Full-length cryo-EM structure of the native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament

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