[English] 日本語
Yorodumi
- EMDB-10515: Phosphorylated turkey beta1 adrenoceptor with bound agonist formo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10515
TitlePhosphorylated turkey beta1 adrenoceptor with bound agonist formoterol coupled to arrestin-2 in lipid nanodisc.
Map data
Sample
  • Complex: Formoterol-bound beta1-adrenoceptor coupled to beta-arrestin-1 stabilised by Fab30.
    • Complex: Beta-1 adrenergic receptor
      • Protein or peptide: Beta-1 adrenergic receptor
    • Complex: Beta-arrestin-1
      • Protein or peptide: Beta-arrestin-1
    • Complex: Fab30 heavy chain
      • Protein or peptide: Fab30 heavy chain
    • Complex: Fab30 light chain
      • Protein or peptide: Fab30 light chain
  • Ligand: ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide
KeywordsGPCR / Arrestin / Complex / Nanodisc / SIGNALING PROTEIN
Function / homology
Function and homology information


beta1-adrenergic receptor activity / positive regulation of heart contraction / angiotensin receptor binding / regulation of circadian sleep/wake cycle, sleep / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / G protein-coupled receptor internalization / arrestin family protein binding / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure ...beta1-adrenergic receptor activity / positive regulation of heart contraction / angiotensin receptor binding / regulation of circadian sleep/wake cycle, sleep / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / G protein-coupled receptor internalization / arrestin family protein binding / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / stress fiber assembly / positive regulation of cardiac muscle hypertrophy / negative regulation of NF-kappaB transcription factor activity / pseudopodium / negative regulation of interleukin-6 production / enzyme inhibitor activity / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / adenylate cyclase-activating adrenergic receptor signaling pathway / clathrin-coated pit / insulin-like growth factor receptor binding / negative regulation of protein ubiquitination / cytoplasmic vesicle membrane / GTPase activator activity / Activated NOTCH1 Transmits Signal to the Nucleus / G protein-coupled receptor binding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / endocytic vesicle membrane / protein transport / Cargo recognition for clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / Clathrin-mediated endocytosis / positive regulation of protein phosphorylation / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / G alpha (s) signalling events / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / early endosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / Ub-specific processing proteases / protein ubiquitination / nuclear body / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Beta 1 adrenoceptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain ...Beta 1 adrenoceptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Adrenoceptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin E-set
Similarity search - Domain/homology
Beta-1 adrenergic receptor / Beta-arrestin-1
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey) / Homo sapiens (human) / Phage display vector pTDisp (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLee Y / Tate CG
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)EMPSI 339995 United Kingdom
Medical Research Council (MRC, United Kingdom)MRC U105197215 United Kingdom
Citation
Journal: Nature / Year: 2020
Title: Molecular basis of β-arrestin coupling to formoterol-bound β-adrenoceptor.
Authors: Yang Lee / Tony Warne / Rony Nehmé / Shubhi Pandey / Hemlata Dwivedi-Agnihotri / Madhu Chaturvedi / Patricia C Edwards / Javier García-Nafría / Andrew G W Leslie / Arun K Shukla / Christopher G Tate /
Abstract: The β-adrenoceptor (βAR) is a G-protein-coupled receptor (GPCR) that couples to the heterotrimeric G protein G. G-protein-mediated signalling is terminated by phosphorylation of the C terminus of ...The β-adrenoceptor (βAR) is a G-protein-coupled receptor (GPCR) that couples to the heterotrimeric G protein G. G-protein-mediated signalling is terminated by phosphorylation of the C terminus of the receptor by GPCR kinases (GRKs) and by coupling of β-arrestin 1 (βarr1, also known as arrestin 2), which displaces G and induces signalling through the MAP kinase pathway. The ability of synthetic agonists to induce signalling preferentially through either G proteins or arrestins-known as biased agonism-is important in drug development, because the therapeutic effect may arise from only one signalling cascade, whereas the other pathway may mediate undesirable side effects. To understand the molecular basis for arrestin coupling, here we determined the cryo-electron microscopy structure of the βAR-βarr1 complex in lipid nanodiscs bound to the biased agonist formoterol, and the crystal structure of formoterol-bound βAR coupled to the G-protein-mimetic nanobody Nb80. βarr1 couples to βAR in a manner distinct to that of G coupling to βAR-the finger loop of βarr1 occupies a narrower cleft on the intracellular surface, and is closer to transmembrane helix H7 of the receptor when compared with the C-terminal α5 helix of G. The conformation of the finger loop in βarr1 is different from that adopted by the finger loop of visual arrestin when it couples to rhodopsin. βAR coupled to βarr1 shows considerable differences in structure compared with βAR coupled to Nb80, including an inward movement of extracellular loop 3 and the cytoplasmic ends of H5 and H6. We observe weakened interactions between formoterol and two serine residues in H5 at the orthosteric binding site of βAR, and find that formoterol has a lower affinity for the βAR-βarr1 complex than for the βAR-G complex. The structural differences between these complexes of βAR provide a foundation for the design of small molecules that could bias signalling in the β-adrenoceptors.
#1: Journal: Biorxiv / Year: 2020
Title: Molecular determinants of beta-arrestin coupling to formoterol-bound beta1-adrenoceptor.
Authors: Lee Y / Warne T / Nehme R / Pandey S / Dwivedi-Agnihotri H / Edwards PC / Garcia-Nafria J / Leslie AGW / Shukla AK / Tate CG
History
DepositionNov 28, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseJun 17, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6tko
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10515.png

Downloads & links

-
Map

FileDownload / File: emd_10515.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.1329306 - 0.2169568
Average (Standard dev.)0.00013055358 (±0.003136853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1330.2170.000

-
Supplemental data

-
Mask #1

Fileemd_10515_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RELION auto-refinement half map 2. Half maps were...

Fileemd_10515_half_map_1.map
AnnotationRELION auto-refinement half map 2. Half maps were locally filtered between refinement iterations using SIDESPLITTER.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RELION auto-refinement half map 1. Half maps were...

Fileemd_10515_half_map_2.map
AnnotationRELION auto-refinement half map 1. Half maps were locally filtered between refinement iterations using SIDESPLITTER.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Formoterol-bound beta1-adrenoceptor coupled to beta-arrestin-1 st...

EntireName: Formoterol-bound beta1-adrenoceptor coupled to beta-arrestin-1 stabilised by Fab30.
Components
  • Complex: Formoterol-bound beta1-adrenoceptor coupled to beta-arrestin-1 stabilised by Fab30.
    • Complex: Beta-1 adrenergic receptor
      • Protein or peptide: Beta-1 adrenergic receptor
    • Complex: Beta-arrestin-1
      • Protein or peptide: Beta-arrestin-1
    • Complex: Fab30 heavy chain
      • Protein or peptide: Fab30 heavy chain
    • Complex: Fab30 light chain
      • Protein or peptide: Fab30 light chain
  • Ligand: ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide

+
Supramolecule #1: Formoterol-bound beta1-adrenoceptor coupled to beta-arrestin-1 st...

SupramoleculeName: Formoterol-bound beta1-adrenoceptor coupled to beta-arrestin-1 stabilised by Fab30.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: Complex formed in lipid nanodisc.
Molecular weightTheoretical: 133 KDa

+
Supramolecule #2: Beta-1 adrenergic receptor

SupramoleculeName: Beta-1 adrenergic receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Meleagris gallopavo (turkey)

+
Supramolecule #3: Beta-arrestin-1

SupramoleculeName: Beta-arrestin-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #4: Fab30 heavy chain

SupramoleculeName: Fab30 heavy chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Phage display vector pTDisp (others)

+
Supramolecule #5: Fab30 light chain

SupramoleculeName: Fab30 light chain / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Phage display vector pTDisp (others)

+
Macromolecule #1: Beta-1 adrenergic receptor

MacromoleculeName: Beta-1 adrenergic receptor / type: protein_or_peptide / ID: 1
Details: Relative to wild-type sequence: construct is truncated at the N-terminus; and in ICL3; its C-terminus is truncated at C358A and fused with a linker to a series of phosphorylated residues ...Details: Relative to wild-type sequence: construct is truncated at the N-terminus; and in ICL3; its C-terminus is truncated at C358A and fused with a linker to a series of phosphorylated residues (ARGRPLPETGGGDE[pS]A[pT][pT]A[pS][pS][pS]LAKDTSS).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Meleagris gallopavo (turkey)
Molecular weightTheoretical: 37.275395 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAELLSQQWE AGCSLLMALV VLLIVAGNVL VIAAIGRTQR LQTLTNLFIT SLACADLVVG LLVVPFGATL VCRGTWLWGS FLCELWTSL DVLCVTASIW TLCVIAIDRY LAITSPFRYQ SLMTRARAKV IICTVWAISA LVSFLPIMMH WWRDEDPQAL K CYQDPGCC ...String:
GAELLSQQWE AGCSLLMALV VLLIVAGNVL VIAAIGRTQR LQTLTNLFIT SLACADLVVG LLVVPFGATL VCRGTWLWGS FLCELWTSL DVLCVTASIW TLCVIAIDRY LAITSPFRYQ SLMTRARAKV IICTVWAISA LVSFLPIMMH WWRDEDPQAL K CYQDPGCC DFVTNRAYAI ASSIISFYIP LLIMIFVYLR VYREAKEQIR KIDRASKRKT SRVMAMREHK ALKTLGIIMG VF TLCWLPF FLVNIVNVFN RDLVPKWLFV AFNWLGYANS AMNPIIYCRS PDFRKAFKRL LAARGRPLPE TGGGDE(SEP)A (TPO) (TPO)A(SEP)(SEP)(SEP)LAKDT SS

UniProtKB: Beta-1 adrenergic receptor

+
Macromolecule #2: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 2
Details: Additional N-terminal Gly residue, in place of starting Met, remaining from proteolytic cleavage.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.021332 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDCDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI ...String:
GGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDCDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI EKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD ICLFNTA QYKCPVAMEE ADDTVAPSST FCKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP ENETPVDTNL IELDTNDDDI VFEDFARQRL KGMK DDKEE EEDGTGSPQL NNR

UniProtKB: Beta-arrestin-1

+
Macromolecule #3: Fab30 heavy chain

MacromoleculeName: Fab30 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phage display vector pTDisp (others)
Molecular weightTheoretical: 25.512354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THHHHHHHH

+
Macromolecule #4: Fab30 light chain

MacromoleculeName: Fab30 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phage display vector pTDisp (others)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

+
Macromolecule #5: ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino...

MacromoleculeName: ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: H98
Molecular weightTheoretical: 344.405 Da
Chemical component information

ChemComp-H98:
~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide / agonist*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
20.0 mMNaClsodium chloride
2.0 uMC21H26N2O2Formoterol hemifumarate
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blotted for 2-3 seconds before plunging. Liquid ethane maintained at 92.15 K..
DetailsThis sample was monodisperse.

-
Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV
DetailsData collected with a stage-tilt of 30deg; two non-overlapping exposures per hole and multi-hole image-shift data acquisition strategies (3x3 holes per stage shift).
Image recordingImage recording ID: 1 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV
DetailsData collected with a stage-tilt of 30deg; two non-overlapping exposures per hole using image-shift.
Image recordingImage recording ID: 2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 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

Image recording ID1
Particle selectionNumber selected: 10161197
Startup modelType of model: OTHER / Details: Ab initio model generated using SGD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: Half maps were locally filtered between refinement iterations using SIDESPLITTER, an adaptation of the LAFTER algorithm that maintains gold-standard separation between the two half maps.
Number images used: 403991
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

6ibl

chain_id: A, residue_range: 41-401, source_name: PDB, initial_model_type: experimental model

4jqi

chain_id: A, residue_range: 6-356, source_name: PDB, initial_model_type: experimental model

4jqi

chain_id: H, residue_range: 5-223, source_name: PDB, initial_model_type: experimental model

4jqi

chain_id: L, residue_range: 1-190, source_name: PDB, initial_model_type: experimental model

4jqi

chain_id: V, residue_range: 356-368, source_name: PDB, initial_model_type: experimental model
DetailsInitial placement was done manually in Coot, followed by rigid-body refinement in PHENIX and jelly-body refinement in REFMAC5. Manual remodeling was performed in Coot and iterated with real space refinement in PHENIX. Chemical restraints for formoterol were calculated in eLBOW using AM1 optimisation.
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 80.6 / Target criteria: Correlation coefficient
Output model

PDB-6tko:
Phosphorylated turkey beta1 adrenoceptor with bound agonist formoterol coupled to arrestin-2 in lipid nanodisc.

+
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