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- PDB-5uz7: Volta phase plate cryo-electron microscopy structure of a calcito... -

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Entry
Database: PDB / ID: 5uz7
TitleVolta phase plate cryo-electron microscopy structure of a calcitonin receptor-heterotrimeric Gs protein complex
DescriptorNanobody 35
Calcitonin receptor
(Guanine nucleotide-binding protein ...) x 3
KeywordsSIGNALING PROTEIN / Class B G protein-coupled receptor Agonist-Receptor-G protein ternary complex Calcitonin receptor Active-state G protein-coupled receptor
Specimen sourceHomo sapiens / human
Lama glama / mammal / ラマ, リャマ /
MethodElectron microscopy (4.1 Å resolution / Particle / Single particle)
AuthorsLiang, Y.L. / Khoshouei, M. / Radjainia, M. / Zhang, Y. / Glukhova, A. / Tarrasch, J. / Thal, D.M. / Furness, S.G.B. / Christopoulos, G. / Coudrat, T. / Danev, R. / Baumeister, W. / Miller, L.J. / Christopoulos, A. / Kobilka, B.K. / Wootten, D. / Skiniotis, G. / Sexton, P.M.
CitationNature, 2017, 546, 118-123

Nature, 2017, 546, 118-123 StrPapers
Phase-plate cryo-EM structure of a class B GPCR-G-protein complex.
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 24, 2017 / Release: May 3, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 3, 2017Structure modelrepositoryInitial release
1.1Jun 14, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N: NANOBODY 35
R: Calcitonin receptor


Theoretical massNumber of molelcules
Total (without water)164,2455
Polyers164,2455
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-stimulating G alpha protein


Mass: 44326.160 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P63092

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 38744.371 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P62873

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7563.750 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P59768

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)NANOBODY 35


Mass: 15140.742 Da / Num. of mol.: 1
Source: (gene. exp.) Lama glama / mammal / ラマ, リャマ /
#5: Polypeptide(L)Calcitonin receptor / CT-R


Mass: 58469.594 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P30988

Cellular component

Molecular function

Biological process

  • adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO: 0007189)
  • amylin receptor signaling pathway (GO: 0097647)
  • cell surface receptor signaling pathway (GO: 0007166)
  • positive regulation of adenylate cyclase activity (GO: 0045762)
  • positive regulation of calcium ion import across plasma membrane (GO: 1905665)
  • positive regulation of cAMP biosynthetic process (GO: 0030819)
  • positive regulation of cAMP metabolic process (GO: 0030816)
  • positive regulation of cell death (GO: 0010942)
  • positive regulation of cytosolic calcium ion concentration (GO: 0007204)
  • positive regulation of ERK1 and ERK2 cascade (GO: 0070374)
  • positive regulation of gene expression (GO: 0010628)
  • positive regulation of peptidyl-serine phosphorylation (GO: 0033138)
  • positive regulation of protein kinase A signaling (GO: 0010739)
  • positive regulation of protein kinase B signaling (GO: 0051897)
  • protein localization to plasma membrane (GO: 0072659)
  • protein transport (GO: 0015031)
  • receptor internalization (GO: 0031623)
  • response to glucocorticoid (GO: 0051384)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Complex of a full-length, active-state calcitonin receptor with peptide ligand, heterotrimeric Gs protein and nano body 35.
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5 / Source: RECOMBINANT
Molecular weightValue: 0.15 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Trichoplusia ni
Buffer solutionpH: 7.5
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifuoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / C2 aperture diameter: 50 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 106838 / Symmetry type: POINT

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