[English] 日本語
Yorodumi
- EMDB-8623: Volta phase plate cryo-electron microscopy structure of a calcito... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8623
TitleVolta phase plate cryo-electron microscopy structure of a calcitonin receptor-heterotrimeric Gs protein complex
Map data
SampleComplex of a full-length, active-state calcitonin receptor with peptide ligand, heterotrimeric Gs protein and nano body 35.
Function/homologyGPCR, family 2, calcitonin receptor / calcitonin binding / calcitonin receptor activity / GPCR, family 2, calcitonin receptor family / Olfactory Signaling Pathway / amylin receptor complex / Thromboxane signalling through TP receptor / Prostacyclin signalling through prostacyclin receptor / Activation of the phototransduction cascade / Presynaptic function of Kainate receptors ...GPCR, family 2, calcitonin receptor / calcitonin binding / calcitonin receptor activity / GPCR, family 2, calcitonin receptor family / Olfactory Signaling Pathway / amylin receptor complex / Thromboxane signalling through TP receptor / Prostacyclin signalling through prostacyclin receptor / Activation of the phototransduction cascade / Presynaptic function of Kainate receptors / G beta:gamma signalling through PLC beta / positive regulation of adenylate cyclase activity / positive regulation of calcium ion import across plasma membrane / G-protein alpha subunit, group S / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Activation of G protein gated Potassium channels / Calcitonin-like ligand receptors / Glucagon signaling in metabolic regulation / amylin receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / G-protein activation / G-protein, gamma subunit / G-protein gamma subunit domain profile. / cellular response to catecholamine stimulus / Adrenaline,noradrenaline inhibits insulin secretion / cardiac muscle cell apoptotic process / G-protein, beta subunit / Guanine nucleotide-binding protein, beta subunit / G-protein gamma-like domain / G-protein gamma-like domain superfamily / intrinsic component of membrane / PKA activation in glucagon signalling / G-protein coupled acetylcholine receptor signaling pathway / G-protein beta-subunit binding / G-protein coupled receptors family 2 signature 1. / G alpha (z) signalling events / protein heterotrimerization / sensory perception of taste / GGL domain / alkylglycerophosphoethanolamine phosphodiesterase activity / adenylate cyclase-activating adrenergic receptor signaling pathway / Glucagon-type ligand receptors / G-protein coupled receptors family 2 profile 1. / GPCR family 2, extracellular hormone receptor domain superfamily / GPCR, family 2, extracellular hormone receptor domain / intracellular transport / GPCR, family 2, secretin-like, conserved site / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like / adenylate cyclase-activating dopamine receptor signaling pathway / 7 transmembrane receptor (Secretin family) / rhodopsin mediated signaling pathway / hair follicle placode formation / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of cAMP-mediated signaling / photoreceptor outer segment membrane / Vasopressin regulates renal water homeostasis via Aquaporins / bone development / Hormone receptor domain / G-protein coupled receptors family 2 profile 2. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / GPCR, family 2-like / spectrin binding / Hedgehog 'off' state / activation of adenylate cyclase activity / sensory perception of smell / G-protein beta/gamma-subunit complex binding / photoreceptor disc membrane / developmental growth / type 1 angiotensin receptor binding / heterotrimeric G-protein complex / adenylate cyclase-activating G-protein coupled receptor signaling pathway / G-protein alpha subunit / positive regulation of cAMP metabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / cellular response to glucagon stimulus / renal water homeostasis / Inactivation, recovery and regulation of the phototransduction cascade / Wnt signaling pathway, calcium modulating pathway / cellular response to prostaglandin E stimulus / extracellular vesicle / positive regulation of protein kinase A signaling / positive regulation of cAMP biosynthetic process / Ca2+ pathway / ADP signalling through P2Y purinoceptor 1 / trans-Golgi network membrane / G alpha (12/13) signalling events / retina development in camera-type eye / phospholipase C-activating G-protein coupled receptor signaling pathway / photoreceptor inner segment / cognition / GTPase binding / regulation of insulin secretion / protein transporter activity / G alpha (s) signalling events / protein localization to plasma membrane / G alpha (i) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / G beta:gamma signalling through PI3Kgamma
Function and homology information
SourceHomo sapiens / human /
Methodsingle particle reconstruction, at 4.1 Å resolution
AuthorsLiang YL / Khoshouei M
CitationJournal: Nature / Year: 2017
Title: Phase-plate cryo-EM structure of a class B GPCR-G-protein complex.
Authors: Yi-Lynn Liang / Maryam Khoshouei / Mazdak Radjainia / Yan Zhang / Alisa Glukhova / Jeffrey Tarrasch / David M Thal / Sebastian G B Furness / George Christopoulos / Thomas Coudrat / Radostin Danev / Wolfgang Baumeister / Laurence J Miller / Arthur Christopoulos / Brian K Kobilka / Denise Wootten / Georgios Skiniotis / Patrick M Sexton
Abstract: Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, such as osteoporosis, diabetes and obesity. Here we report the structure of a full-length class B ...Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, such as osteoporosis, diabetes and obesity. Here we report the structure of a full-length class B receptor, the calcitonin receptor, in complex with peptide ligand and heterotrimeric Gαβγ protein determined by Volta phase-plate single-particle cryo-electron microscopy. The peptide agonist engages the receptor by binding to an extended hydrophobic pocket facilitated by the large outward movement of the extracellular ends of transmembrane helices 6 and 7. This conformation is accompanied by a 60° kink in helix 6 and a large outward movement of the intracellular end of this helix, opening the bundle to accommodate interactions with the α5-helix of Gα. Also observed is an extended intracellular helix 8 that contributes to both receptor stability and functional G-protein coupling via an interaction with the Gβ subunit. This structure provides a new framework for understanding G-protein-coupled receptor function.
Validation ReportPDB-ID: 5uz7

SummaryFull reportAbout validation report
DateDeposition: Feb 24, 2017 / Header (metadata) release: Mar 29, 2017 / Map release: May 3, 2017 / Last update: Jun 14, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5uz7
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links

-
Map

Fileemd_8623.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.06 Å/pix.
= 212. Å
200 pix
1.06 Å/pix.
= 212. Å
200 pix
1.06 Å/pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.05 (by author), 0.04 (movie #1):
Minimum - Maximum-0.14220421 - 0.2546117
Average (Standard dev.)0.00021038976 (0.008024996)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90 deg.

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/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1420.2550.000

-
Supplemental data

-
Sample components

+
Entire Complex of a full-length, active-state calcitonin receptor with p...

EntireName: Complex of a full-length, active-state calcitonin receptor with peptide ligand, heterotrimeric Gs protein and nano body 35.
Number of components: 6
MassTheoretical: 150 kDa

+
Component #1: protein, Complex of a full-length, active-state calcitonin recept...

ProteinName: Complex of a full-length, active-state calcitonin receptor with peptide ligand, heterotrimeric Gs protein and nano body 35.
Recombinant expression: No
MassTheoretical: 150 kDa
SourceSpecies: Homo sapiens / human /
Source (engineered)Expression System: Trichoplusia ni / arthropod / Cabbage looper

+
Component #2: protein, Guanine nucleotide-binding protein G(s) subunit alpha is...

ProteinName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Recombinant expression: No
MassTheoretical: 44.32616 kDa
Source (engineered)Expression System: Homo sapiens / human /

+
Component #3: protein, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subuni...

ProteinName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Recombinant expression: No
MassTheoretical: 38.744371 kDa
Source (engineered)Expression System: Homo sapiens / human /

+
Component #4: protein, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subuni...

ProteinName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Recombinant expression: No
MassTheoretical: 7.56375 kDa
Source (engineered)Expression System: Homo sapiens / human /

+
Component #5: protein, NANOBODY 35

ProteinName: NANOBODY 35 / Recombinant expression: No
MassTheoretical: 15.140742 kDa
Source (engineered)Expression System: Lama glama / mammal / Llama /

+
Component #6: protein, Calcitonin receptor

ProteinName: Calcitonin receptor / Recombinant expression: No
MassTheoretical: 58.469594 kDa
Source (engineered)Expression System: Homo sapiens / human /

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.3 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 106838
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more