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- EMDB-17343: Cryo-EM structure of Rhodopsin-Gi bound to antibody fragment Fab13 -

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Basic information

Entry
Database: EMDB / ID: EMD-17343
TitleCryo-EM structure of Rhodopsin-Gi bound to antibody fragment Fab13
Map dataRho-Gi-Fab13
Sample
  • Complex: Rhodopsin-Gi-Fab13 complex
    • Complex: Rhodopsin
      • Protein or peptide: Rhodopsin
    • Complex: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 and Guanine nucleotide-binding protein G(T) subunit gamma-T1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(T) subunit gamma-T1
    • Complex: Immunoglobin G light chain and Immunoglobin G heavy chain FAB fragment
      • Protein or peptide: Immunoglobin G light chain
      • Protein or peptide: Immunoglobin G heavy chain FAB fragment
KeywordsGPCR / Rhodopsin / G protein / Fab / SIGNALING PROTEIN
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / Olfactory Signaling Pathway / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane ...Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / Olfactory Signaling Pathway / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / podosome assembly / G protein-coupled photoreceptor activity / 11-cis retinal binding / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / rod photoreceptor outer segment / cellular response to light stimulus / eye photoreceptor cell development / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / response to light intensity / photoreceptor cell maintenance / arrestin family protein binding / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / photoreceptor outer segment membrane / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / phototransduction, visible light / response to light stimulus / photoreceptor outer segment / phototransduction / G-protein alpha-subunit binding / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / sperm midpiece / visual perception / cellular response to forskolin / regulation of mitotic spindle organization / guanyl-nucleotide exchange factor activity / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to peptide hormone / G-protein beta/gamma-subunit complex binding / centriolar satellite / microtubule cytoskeleton organization / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / GDP binding / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / intracellular protein localization / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / cell-cell junction / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / G protein activity / GTPase binding / retina development in camera-type eye
Similarity search - Function
Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit ...Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(T) subunit gamma-T1 / Rhodopsin / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsPamula F / Tejero O / Muehle J / Thoma R / Schertler GFX / Marino J / Tsai C-J
Funding support Switzerland, European Union, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation173335 Switzerland
Swiss National Science Foundation153145 Switzerland
Swiss National Science Foundation192760 Switzerland
European Research Council (ERC)951644European Union
CitationJournal: To Be Published
Title: Characterization of two novel antibody fragments for obtaining cryo-EM structures of GPCR-G protein complexes
Authors: Pamula F / Tejero O / Muehle J / Thoma R / Schertler GFX / Marino J / Tsai C-J
History
DepositionMay 11, 2023-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17343.png

Downloads & links

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Map

FileDownload / File: emd_17343.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRho-Gi-Fab13
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 300 pix.
= 390. Å		1.3 Å/pix.
x 300 pix.
= 390. Å		1.3 Å/pix.
x 300 pix.
= 390. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.5721611 - 1.4195912
Average (Standard dev.)-0.0010088998 (±0.019488603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 390.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_17343_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_17343_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rhodopsin-Gi-Fab13 complex

EntireName: Rhodopsin-Gi-Fab13 complex
Components
  • Complex: Rhodopsin-Gi-Fab13 complex
    • Complex: Rhodopsin
      • Protein or peptide: Rhodopsin
    • Complex: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 and Guanine nucleotide-binding protein G(T) subunit gamma-T1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(T) subunit gamma-T1
    • Complex: Immunoglobin G light chain and Immunoglobin G heavy chain FAB fragment
      • Protein or peptide: Immunoglobin G light chain
      • Protein or peptide: Immunoglobin G heavy chain FAB fragment

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Supramolecule #1: Rhodopsin-Gi-Fab13 complex

SupramoleculeName: Rhodopsin-Gi-Fab13 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: bovine rhodopsin N2C/M257Y/D282C
Molecular weightTheoretical: 170 KDa

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Supramolecule #2: Rhodopsin

SupramoleculeName: Rhodopsin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1

SupramoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 ...

SupramoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 and Guanine nucleotide-binding protein G(T) subunit gamma-T1
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #5: Immunoglobin G light chain and Immunoglobin G heavy chain FAB fragment

SupramoleculeName: Immunoglobin G light chain and Immunoglobin G heavy chain FAB fragment
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Rhodopsin

MacromoleculeName: Rhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Cell: rod photoreceptor cell
Molecular weightTheoretical: 39.040527 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MCGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFG GFTTTLYTSL HGYFVFGPTG CNLEGFFATL GGEIALWSLV VLAIERYVVV CKPMSNFRFG ENHAIMGVAF T WVMALACA ...String:
MCGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFG GFTTTLYTSL HGYFVFGPTG CNLEGFFATL GGEIALWSLV VLAIERYVVV CKPMSNFRFG ENHAIMGVAF T WVMALACA APPLVGWSRY IPEGMQCSCG IDYYTPHEET NNESFVIYMF VVHFIIPLIV IFFCYGQLVF TVKEAAAQQQ ES ATTQKAE KEVTRMVIIY VIAFLICWLP YAGVAFYIFT HQGSCFGPIF MTIPAFFAKT SAVYNPVIYI MMNKQFRNCM VTT LCCGKN PLGDDEASTT VSKTETSQVA PA

UniProtKB: Rhodopsin

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Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.182078 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKKHHHHHHH HHHENLYFQG GSMGCTLSAE DKAAVERSKM IDRNLREDGE KAAREVKLLL LGAGESGKST IVKQMKIIHE AGYSEEECK QYKAVVYSNT IQSIIAIIRA MGRLKIDFGD SARADDARQL FVLAGAAEEG FMTAELAGVI KRLWKDSGVQ A CFNRSREY ...String:
MKKHHHHHHH HHHENLYFQG GSMGCTLSAE DKAAVERSKM IDRNLREDGE KAAREVKLLL LGAGESGKST IVKQMKIIHE AGYSEEECK QYKAVVYSNT IQSIIAIIRA MGRLKIDFGD SARADDARQL FVLAGAAEEG FMTAELAGVI KRLWKDSGVQ A CFNRSREY QLNDSAAYYL NDLDRIAQPN YIPTQQDVLR TRVKTTGIVE THFTFKDLHF KMFDVGGQRS ERKKWIHCFE GV TAIIFCV ALSDYDLVLA EDEEMNRMHE SMKLFDSICN NKWFTDTSII LFLNKKDLFE EKIKKSPLTI CYPEYAGSNT YEE AAAYIQ CQFEDLNKRK DTKEIYTHFT CATDTKNVQF VFDAVTDVII KNNLKDCGLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: Eye / Tissue: retina
Molecular weightTheoretical: 37.41693 KDa
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #4: Guanine nucleotide-binding protein G(T) subunit gamma-T1

MacromoleculeName: Guanine nucleotide-binding protein G(T) subunit gamma-T1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: eye / Tissue: retina
Molecular weightTheoretical: 8.556918 KDa
SequenceString:
MPVINIEDLT EKDKLKMEVD QLKKEVTLER MLVSKCCEEF RDYVEERSGE DPLVKGIPED KNPFKELKGG CVIS

UniProtKB: Guanine nucleotide-binding protein G(T) subunit gamma-T1

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Macromolecule #5: Immunoglobin G light chain

MacromoleculeName: Immunoglobin G light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.349555 KDa
SequenceString: MKLPVRLLVL MFWIPASSSD VLMTQTPLSL PVSLGDQASI SCRSSQIIVN RNGNTYLEWY LQKPGQSPKL LIYKVSNRFS GVPDRFSGS GSGTDFTLKI SGVEAEDLGV YYCFQGSHVP WTFGGGTQLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI ...String:
MKLPVRLLVL MFWIPASSSD VLMTQTPLSL PVSLGDQASI SCRSSQIIVN RNGNTYLEWY LQKPGQSPKL LIYKVSNRFS GVPDRFSGS GSGTDFTLKI SGVEAEDLGV YYCFQGSHVP WTFGGGTQLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI NVKWKIDGSE RQNGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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Macromolecule #6: Immunoglobin G heavy chain FAB fragment

MacromoleculeName: Immunoglobin G heavy chain FAB fragment / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.448336 KDa
SequenceString: MAVLVLFLCL VAFPSCVLSQ VQLKESGPGL VAPSQSLSIT CTVSGFSLTN YGVHWVRQPP GKGLEWLGII WAGGGTSYDS ALMSRLSIS KDNSKSQVFL KMNSLQSTDT AMYYCASENY SYDRGFAYWG QGTLVTVSAA KTTPPSVYPL APGSAAQTNS M VTLGCLVK ...String:
MAVLVLFLCL VAFPSCVLSQ VQLKESGPGL VAPSQSLSIT CTVSGFSLTN YGVHWVRQPP GKGLEWLGII WAGGGTSYDS ALMSRLSIS KDNSKSQVFL KMNSLQSTDT AMYYCASENY SYDRGFAYWG QGTLVTVSAA KTTPPSVYPL APGSAAQTNS M VTLGCLVK GYFPEPVTVT WNSGSLSSGV HTFPAVLQSD LYTLSSSVTV PSSTWPSETV TCNVAHPASS TKVDKKIVPR DC GCKPCIC TVPEVSSVFI F

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride

Details: 20 mM HEPES (pH 7.5), 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodispersed

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3752145
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 587113
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChain

5en0

chain_id: R, source_name: PDB, initial_model_type: experimental model

6cmo

chain_id: A, residue_range: 1-32, source_name: PDB, initial_model_type: experimental model

6crk

chain_id: A, residue_range: 33-323, source_name: PDB, initial_model_type: experimental model

6cmo

chain_id: A, residue_range: 324-354, source_name: PDB, initial_model_type: experimental model

1got

chain_id: B, source_name: PDB, initial_model_type: experimental model

1got

chain_id: G, source_name: PDB, initial_model_type: experimental model
chain_id: L, source_name: AlphaFold, initial_model_type: in silico model
chain_id: H, source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 150 / Target criteria: cross-correlation coefficient
Output model

PDB-8p12:
Cryo-EM structure of Rhodopsin-Gi bound to antibody fragment Fab13

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