[English] 日本語
Yorodumi
- EMDB-11985: TRPC4 in complex with Calmodulin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11985
TitleTRPC4 in complex with Calmodulin
Map data
Sample
  • Organelle or cellular component: TRPC4 membrane protein in complex with calmodulin
    • Organelle or cellular component: Transient receptor potential cation channel subfamily c member 4a
      • Protein or peptide: Transient receptor potential cation channel subfamily c member 4a
    • Organelle or cellular component: Calmodulin-1
      • Protein or peptide: Calmodulin-1
  • Ligand: CALCIUM ION
  • Ligand: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate
KeywordsION CHANNEL / TRPC4 / COMPLEX / MEMBRANE PROTEIN / CALMODULIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation ...CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Ion transport by P-type ATPases / Calcineurin activates NFAT / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / RAF activation / VEGFR2 mediated vascular permeability / RAS processing / presynaptic endocytosis / Ca2+ pathway / Smooth Muscle Contraction / Extra-nuclear estrogen signaling / FCERI mediated Ca+2 mobilization / RHO GTPases activate IQGAPs / RAF/MAP kinase cascade / store-operated calcium channel activity / PKA activation / Platelet degranulation / cation channel complex / Stimuli-sensing channels / Ion homeostasis / type 3 metabotropic glutamate receptor binding / inositol 1,4,5 trisphosphate binding / organelle localization by membrane tethering / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / regulation of cardiac muscle cell action potential / nitric-oxide synthase binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / monoatomic cation transport / adenylate cyclase binding / calyx of Held / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / voltage-gated potassium channel complex / monoatomic cation channel activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / sperm midpiece / regulation of cytosolic calcium ion concentration / calcium channel complex / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / calcium ion transmembrane transport / cellular response to type II interferon / spindle pole / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / transmembrane transporter binding / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / : / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / ankyrin repeats ...Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / : / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / ankyrin repeats / Ankyrin repeat / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Transient receptor potential cation channel subfamily c member 4a
Similarity search - Component
Biological speciesDanio rerio (zebrafish) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsVinayagam D / Quentin D
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Elife / Year: 2020
Title: Structural basis of TRPC4 regulation by calmodulin and pharmacological agents.
Authors: Deivanayagabarathy Vinayagam / Dennis Quentin / Jing Yu-Strzelczyk / Oleg Sitsel / Felipe Merino / Markus Stabrin / Oliver Hofnagel / Maolin Yu / Mark W Ledeboer / Georg Nagel / Goran ...Authors: Deivanayagabarathy Vinayagam / Dennis Quentin / Jing Yu-Strzelczyk / Oleg Sitsel / Felipe Merino / Markus Stabrin / Oliver Hofnagel / Maolin Yu / Mark W Ledeboer / Georg Nagel / Goran Malojcic / Stefan Raunser /
Abstract: Canonical transient receptor potential channels (TRPC) are involved in receptor-operated and/or store-operated Ca signaling. Inhibition of TRPCs by small molecules was shown to be promising in ...Canonical transient receptor potential channels (TRPC) are involved in receptor-operated and/or store-operated Ca signaling. Inhibition of TRPCs by small molecules was shown to be promising in treating renal diseases. In cells, the channels are regulated by calmodulin (CaM). Molecular details of both CaM and drug binding have remained elusive so far. Here, we report structures of TRPC4 in complex with three pyridazinone-based inhibitors and CaM. The structures reveal that all the inhibitors bind to the same cavity of the voltage-sensing-like domain and allow us to describe how structural changes from the ligand-binding site can be transmitted to the central ion-conducting pore of TRPC4. CaM binds to the rib helix of TRPC4, which results in the ordering of a previously disordered region, fixing the channel in its closed conformation. This represents a novel CaM-induced regulatory mechanism of canonical TRP channels.
History
DepositionNov 24, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0052
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0052
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7b1g
  • Surface level: 0.0052
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11985.png

Downloads & links

-
Map

FileDownload / File: emd_11985.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 288 pix.
= 244.8 Å		0.85 Å/pix.
x 288 pix.
= 244.8 Å		0.85 Å/pix.
x 288 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0052 / Movie #1: 0.0052
Minimum - Maximum-0.013438393 - 0.023819605
Average (Standard dev.)0.00013845753 (±0.0009158334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z244.800244.800244.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0130.0240.000

-
Supplemental data

-
Sample components

-
Entire : TRPC4 membrane protein in complex with calmodulin

EntireName: TRPC4 membrane protein in complex with calmodulin
Components
  • Organelle or cellular component: TRPC4 membrane protein in complex with calmodulin
    • Organelle or cellular component: Transient receptor potential cation channel subfamily c member 4a
      • Protein or peptide: Transient receptor potential cation channel subfamily c member 4a
    • Organelle or cellular component: Calmodulin-1
      • Protein or peptide: Calmodulin-1
  • Ligand: CALCIUM ION
  • Ligand: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate

-
Supramolecule #1: TRPC4 membrane protein in complex with calmodulin

SupramoleculeName: TRPC4 membrane protein in complex with calmodulin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: TRPC4 was solubilised in LMNG detergent
Molecular weightTheoretical: 126 KDa

-
Supramolecule #2: Transient receptor potential cation channel subfamily c member 4a

SupramoleculeName: Transient receptor potential cation channel subfamily c member 4a
type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish) / Location in cell: plasma membrane

-
Supramolecule #3: Calmodulin-1

SupramoleculeName: Calmodulin-1 / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Transient receptor potential cation channel subfamily c member 4a

MacromoleculeName: Transient receptor potential cation channel subfamily c member 4a
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 105.204641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSQLYFRRTD NSSYRDRIPL RIVRAESELS TQEKSYLSAV EKGDYASVKL ALEEAEIYFK ININCIDPLG RTALLIAIEN ENLEIIELL LSFNVYVGDA LLHAIRKEVV GAVELLLNHK KPSGEKQVPP ILLDKQFSDF TPDITPIILA AHTNNYEIIK M LVQKGVSV ...String:
GSQLYFRRTD NSSYRDRIPL RIVRAESELS TQEKSYLSAV EKGDYASVKL ALEEAEIYFK ININCIDPLG RTALLIAIEN ENLEIIELL LSFNVYVGDA LLHAIRKEVV GAVELLLNHK KPSGEKQVPP ILLDKQFSDF TPDITPIILA AHTNNYEIIK M LVQKGVSV PQPHEVRCNC VECVSSSDVD SLRHSRSRLN IYKALASPSL IALSSEDPFL TAFQLSWELQ ELSKVENEFK AE YEELSHQ CKHFAKDLLD QTRSSRELEL ILNFRDDMNL LQDEANNELA RLKLAIKYRQ KEFVAQPNCQ QLLASRWYDE FPG WRRRHW AGKLITCVFI GLMFPLLSLC YLVAPKSRYG LFIRKPFIKF ICHTASYLTF LFLLLLASQH IVSNNPDRQG PKPT TVEWM ILPWVLGFIW TEIKQMWDGG FQDYIHDWWN LMDFVMNSLY LATISLKIVA YVKYSGCKPR DTWEMWHPTL VAEAV FAIA NIFSSLRLIS LFTANSHLGP LQISLGRMLL DILKFLFIYC LVLLAFANGL NQLYFYYENS EGMTCKGIRC ERQNNA FST LFETLQSLFW SIFGLISLYV TNVKADHKFT EFVGATMFGT YNVISLVVLL NMLIAMMNNS YQHIADHADI EWKFART KL WMSYFEEGGT LPPPFNIIPS PKSICYLITW IKVHVFKRRS KRTETFGTLG RRAAENVRLN HQYQEVLRNL VKRYVAAM I RDAKTEEGLT EENFKELKQD ISSFRYEVIG MMKGNRKSTR ANKSDTSASD VSHPEGSLQY SSALKQNSKL HLYDVTTAL QQQNSEEAKA SLGCLANGSA VVLTEPILKD KARSDFPKDF TDFGLFPKKQ NPNKIYSLAE EATESDPDIL DWGKEDKPLA GKVEQDVNE SKCLMEEDER VLEEQEMEHI ASSHEH

UniProtKB: Transient receptor potential cation channel subfamily c member 4a

-
Macromolecule #2: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 16.852545 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

UniProtKB: Calmodulin-1

-
Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #4: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate

MacromoleculeName: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / type: ligand / ID: 4 / Number of copies: 4 / Formula: 44E
Molecular weightTheoretical: 368.36 Da
Chemical component information

ChemComp-44E:
(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.35 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3TRIS
150.0 mMNaClsodium chloride
0.003 percentC47H88O26LMNG
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 160.0 K / Max: 190.0 K
Specialist opticsSpherical aberration corrector: Cs corrector first generation
Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-80 / Number grids imaged: 1 / Number real images: 7972 / Average exposure time: 10.0 sec. / Average electron dose: 88.52 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 59000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.5 µm / 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

+
Image processing

Particle selectionNumber selected: 678331
Startup modelType of model: EMDB MAP
EMDB ID:

4339

Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Software - details: MERIDIEN / Number images used: 160829
Initial angle assignmentType: NOT APPLICABLE / Details: Used EMD-4339 as a reference
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE / Software - details: MERIDIEN
Final 3D classificationNumber classes: 10 / Software - Name: SPHIRE (ver. 1.3) / Software - details: SORT3D
Details: Symmetry expansion was used to quadruple the Particles. From the best classes after 3d classification duplicates were removed that resulted in 160829 particles

-
Atomic model buiding 1

Initial model
PDB IDChain

6gik

source_name: PDB, initial_model_type: experimental model

2lv6

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 58.04 / Target criteria: Correlation coefficient
Output model

PDB-7b1g:
TRPC4 in complex with Calmodulin

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more