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- EMDB-7967: Calmodulin-bound full-length rbTRPV5 -

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Basic information

Entry
Database: EMDB / ID: 7967
TitleCalmodulin-bound full-length rbTRPV5
Map dataCalmodulin-bound rbTRPV5
SampleCalmodulin-bound rbTRPV5 tetramer
  • rbTRPV5 tetramer
  • rat Calmodulin
  • Transient receptor potential cation channel subfamily V member 5
  • Calmodulin-1
  • ligand
Function / homologyEF-hand calcium-binding domain. / Transient receptor potential cation channel subfamily V / Ankyrin repeat profile. / EF-hand domain / Ankyrin repeat / Ion transport domain / Transient receptor potential cation channel subfamily V member 5/6 / Transient receptor potential cation channel subfamily V member 5 / EF-hand domain pair / EF-Hand 1, calcium-binding site ...EF-hand calcium-binding domain. / Transient receptor potential cation channel subfamily V / Ankyrin repeat profile. / EF-hand domain / Ankyrin repeat / Ion transport domain / Transient receptor potential cation channel subfamily V member 5/6 / Transient receptor potential cation channel subfamily V member 5 / EF-hand domain pair / EF-Hand 1, calcium-binding site / Ankyrin repeat-containing domain / EF-hand calcium-binding domain profile. / in:ipr004729: / Ankyrin repeat-containing domain superfamily / EF-hand domain pair / Calmodulin / Ion transport protein / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / regulation of store-operated calcium channel activity / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel regulator activity / regulation of urine volume / establishment of protein localization to membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to mitochondrial membrane / positive regulation by host of symbiont cAMP-mediated signal transduction / N-terminal myristoylation domain binding / regulation of synaptic vesicle endocytosis / regulation of high voltage-gated calcium channel activity / protein phosphatase activator activity / adenylate cyclase activator activity / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / catalytic complex / activation of adenylate cyclase activity / adenylate cyclase binding / enzyme regulator activity / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / voltage-gated potassium channel complex / calcium channel activity / calcium channel inhibitor activity / nitric-oxide synthase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of phosphoprotein phosphatase activity / calcium channel complex / calcium ion transmembrane transport / sarcomere / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / calcium ion transport / response to amphetamine / regulation of heart rate / phosphatidylinositol 3-kinase binding / calcium-mediated signaling / positive regulation of DNA binding / spindle microtubule / regulation of cytokinesis / regulation of synaptic vesicle exocytosis / nitric-oxide synthase regulator activity / calcium-dependent protein binding / spindle pole / protein tetramerization / positive regulation of nitric-oxide synthase activity / growth cone / protein homotetramerization / disordered domain specific binding / G2/M transition of mitotic cell cycle / apical plasma membrane / protein N-terminus binding / ion channel binding / calmodulin binding / neuron projection / centrosome / myelin sheath / protein domain specific binding / protein kinase binding / calcium ion binding / integral component of plasma membrane / mitochondrion / nucleoplasm / plasma membrane / nucleus / metal ion binding / cytosol / cytoplasm / Calmodulin-1 / Transient receptor potential cation channel subfamily V member 5
Function and homology information
SourceOryctolagus cuniculus (rabbit) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 4.4 Å resolution
AuthorsHughes TET / Pumroy RA / Moiseenkova-Bell VY
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights on TRPV5 gating by endogenous modulators.
Authors: Taylor E T Hughes / Ruth A Pumroy / Aysenur Torun Yazici / Marina A Kasimova / Edwin C Fluck / Kevin W Huynh / Amrita Samanta / Sudheer K Molugu / Z Hong Zhou / Vincenzo Carnevale / Tibor Rohacs / Vera Y Moiseenkova-Bell
Validation ReportPDB-ID: 6dmw

SummaryFull reportAbout validation report
DateDeposition: Jun 5, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Oct 24, 2018 / Last update: Oct 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0571
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0571
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6dmw
  • Surface level: 0.0571
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7967.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.1 Å/pix.
= 211.2 Å
192 pix
1.1 Å/pix.
= 211.2 Å
192 pix
1.1 Å/pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:0.0571 (by author), 0.0571 (movie #1):
Minimum - Maximum-0.118438095 - 0.21366055
Average (Standard dev.)0.0032627468 (0.014940131)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin0.00.00.0
Limit191.0191.0191.0
Spacing192192192
CellA=B=C: 211.20001 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z211.200211.200211.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.1180.2140.003

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Supplemental data

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Sample components

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Entire Calmodulin-bound rbTRPV5 tetramer

EntireName: Calmodulin-bound rbTRPV5 tetramer / Number of components: 6

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Component #1: protein, Calmodulin-bound rbTRPV5 tetramer

ProteinName: Calmodulin-bound rbTRPV5 tetramer / Recombinant expression: No

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Component #2: protein, rbTRPV5 tetramer

ProteinName: rbTRPV5 tetramer / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #3: protein, rat Calmodulin

ProteinName: rat Calmodulin / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Transient receptor potential cation channel subfamily V ...

ProteinName: Transient receptor potential cation channel subfamily V member 5
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 82.899656 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #5: protein, Calmodulin-1

ProteinName: Calmodulin-1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.852545 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8.800000000000001
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 47484
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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