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- PDB-7jsn: Structure of the Visual Signaling Complex between Transducin and ... -

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Entry
Database: PDB / ID: 7jsn
TitleStructure of the Visual Signaling Complex between Transducin and Phosphodiesterase 6
Components
  • (Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit ...) x 2
  • Guanine nucleotide-binding protein G(t) subunit alpha-1, Guanine nucleotide-binding protein G(i) subunit alpha-1 chimera
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
KeywordsSIGNALING PROTEIN / G protein / G protein-effector complex / Transducin / phosphodiesterase 6 / phototransduction / GPCR signaling
Function / homology
Function and homology information


negative regulation of cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / ion binding / acyl binding / Ca2+ pathway / response to stimulus ...negative regulation of cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / ion binding / acyl binding / Ca2+ pathway / response to stimulus / positive regulation of epidermal growth factor receptor signaling pathway / photoreceptor outer segment membrane / G alpha (i) signalling events / entrainment of circadian clock by photoperiod / 3',5'-cyclic-GMP phosphodiesterase activity / response to light stimulus / phototransduction / cGMP binding / 3',5'-cyclic-nucleotide phosphodiesterase activity / photoreceptor inner segment / visual perception / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / retina development in camera-type eye / positive regulation of MAPK cascade / molecular adaptor activity / GTPase activity / GTP binding / protein kinase binding / signal transduction / zinc ion binding / metal ion binding
Similarity search - Function
Retinal cGMP phosphodiesterase, gamma subunit / Retinal cGMP phosphodiesterase, gamma subunit superfamily / Retinal cGMP phosphodiesterase, gamma subunit / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / Domain present in phytochromes and cGMP-specific phosphodiesterases. / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase ...Retinal cGMP phosphodiesterase, gamma subunit / Retinal cGMP phosphodiesterase, gamma subunit superfamily / Retinal cGMP phosphodiesterase, gamma subunit / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / Domain present in phytochromes and cGMP-specific phosphodiesterases. / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-3',5'-MONOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-VDN / Guanine nucleotide-binding protein G(t) subunit alpha-1 / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma / Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha / Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGao, Y. / Eskici, G. / Ramachandran, S. / Skiniotis, G. / Cerione, R.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM122575 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA201402 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS092695 United States
CitationJournal: Mol Cell / Year: 2020
Title: Structure of the Visual Signaling Complex between Transducin and Phosphodiesterase 6.
Authors: Yang Gao / Gözde Eskici / Sekar Ramachandran / Frédéric Poitevin / Alpay Burak Seven / Ouliana Panova / Georgios Skiniotis / Richard A Cerione /
Abstract: Heterotrimeric G proteins communicate signals from activated G protein-coupled receptors to downstream effector proteins. In the phototransduction pathway responsible for vertebrate vision, the G ...Heterotrimeric G proteins communicate signals from activated G protein-coupled receptors to downstream effector proteins. In the phototransduction pathway responsible for vertebrate vision, the G protein-effector complex is composed of the GTP-bound transducin α subunit (Gα·GTP) and the cyclic GMP (cGMP) phosphodiesterase 6 (PDE6), which stimulates cGMP hydrolysis, leading to hyperpolarization of the photoreceptor cell. Here we report a cryo-electron microscopy (cryoEM) structure of PDE6 complexed to GTP-bound Gα. The structure reveals two Gα·GTP subunits engaging the PDE6 hetero-tetramer at both the PDE6 catalytic core and the PDEγ subunits, driving extensive rearrangements to relieve all inhibitory constraints on enzyme catalysis. Analysis of the conformational ensemble in the cryoEM data highlights the dynamic nature of the contacts between the two Gα·GTP subunits and PDE6 that supports an alternating-site catalytic mechanism.
History
DepositionAug 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Mar 31, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_ls_restr / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _entity.formula_weight / _entity.pdbx_description ..._entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _entity_src_gen.entity_id / _entity_src_nat.entity_id / _pdbx_entry_details.has_ligand_of_interest / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id
Description: Model orientation/position / Provider: author / Type: Coordinate replacement

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Structure visualization

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Assembly

Deposited unit
A: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha
B: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
E: Guanine nucleotide-binding protein G(t) subunit alpha-1, Guanine nucleotide-binding protein G(i) subunit alpha-1 chimera
F: Guanine nucleotide-binding protein G(t) subunit alpha-1, Guanine nucleotide-binding protein G(i) subunit alpha-1 chimera
C: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
D: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,60916
Polymers301,7166
Non-polymers2,89310
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area29960 Å2
ΔGint-247 kcal/mol
Surface area119960 Å2

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Components

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Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit ... , 2 types, 2 molecules AB

#1: Protein Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha / GMP-PDE alpha / PDE V-B1


Mass: 99461.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P11541, 3',5'-cyclic-GMP phosphodiesterase
#2: Protein Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta / GMP-PDE beta


Mass: 98449.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P23439, 3',5'-cyclic-GMP phosphodiesterase

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Protein , 2 types, 4 molecules EFCD

#3: Protein Guanine nucleotide-binding protein G(t) subunit alpha-1, Guanine nucleotide-binding protein G(i) subunit alpha-1 chimera / Transducin alpha-1 chain


Mass: 42218.035 Da / Num. of mol.: 2 / Mutation: R174C,Q200L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GNAT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04695, UniProt: P04972*PLUS
#4: Protein Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma / GMP-PDE gamma


Mass: 9684.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P04972, UniProt: P04695*PLUS, 3',5'-cyclic-GMP phosphodiesterase

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Non-polymers , 5 types, 10 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-VDN / 2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE / VARDENAFIL, LEVITRA / Vardenafil


Mass: 488.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H32N6O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#8: Chemical ChemComp-35G / GUANOSINE-3',5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O7P
#9: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of Transducin and Phosphodiesterase 6COMPLEX#1-#40MULTIPLE SOURCES
2Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha (E.C.3.1.4.35), Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta (E.C.3.1.4.35), Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (E.C.3.1.4.35)COMPLEX#1-#31NATURAL
3Guanine nucleotide-binding protein G(t) subunit alpha-1, Guanine nucleotide-binding protein G(i) subunit alpha-1 chimera,Gt-alpha/Gi1-alpha chimeraCOMPLEX#41RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bos taurus (cattle)9913
23Bos taurus (cattle)9913
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 20 mM Tris pH 8.0, 5 mM MgCl2 and 1 uM vardenafil
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.05% octyl glucoside was used as an additive.
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingAverage exposure time: 4 sec. / Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143125 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00419865
ELECTRON MICROSCOPYf_angle_d0.55726886
ELECTRON MICROSCOPYf_dihedral_angle_d14.5297380
ELECTRON MICROSCOPYf_chiral_restr0.0432948
ELECTRON MICROSCOPYf_plane_restr0.0043439

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