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- EMDB-17345: Cryo-EM structure of Rhodopsin-Gi bound with antibody fragments s... -

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Basic information

Entry
Database: EMDB / ID: EMD-17345
TitleCryo-EM structure of Rhodopsin-Gi bound with antibody fragments scFv16 and Fab79, conformation 2
Map data
Sample
  • Complex: Rhodopsin-Gi-scFv16-Fab79 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: single-chain Fv scFv16
      • Protein or peptide: single-chain Fv scFv16
    • Complex: Immunoglobin G heavy chain FAB fragment and Immunoglobin G light chain
      • Protein or peptide: Immunoglobin G heavy chain FAB fragment
      • Protein or peptide: Immunoglobin G light chain
KeywordsGPCR / Rhodopsin / G protein / Fab / SIGNALING PROTEIN
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / sperm head plasma membrane / opsin binding / The canonical retinoid cycle in rods (twilight vision) / absorption of visible light / G protein-coupled opsin signaling pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste ...Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / sperm head plasma membrane / opsin binding / The canonical retinoid cycle in rods (twilight vision) / absorption of visible light / G protein-coupled opsin signaling pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / 11-cis retinal binding / podosome assembly / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / cellular response to light stimulus / rod photoreceptor outer segment / 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 / G alpha (z) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / photoreceptor outer segment membrane / 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 / phototransduction / response to light stimulus / photoreceptor outer segment / G-protein alpha-subunit binding / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / T cell migration / positive regulation of relaxation of smooth muscle / Adenylate cyclase inhibitory pathway / D2 dopamine receptor binding / visual perception / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / guanyl-nucleotide exchange factor activity / cellular response to forskolin / regulation of mitotic spindle organization / chemokine-mediated signaling pathway / neuropeptide signaling pathway / Regulation of insulin secretion / response to prostaglandin E / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / response to peptide hormone / microtubule cytoskeleton organization / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / centriolar satellite / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cell-cell junction / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / GDP binding / intracellular protein localization / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / sperm principal piece
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 / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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: 5.9 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: Biophys J / Year: 2025
Title: Tool antibody fragments reveal multiple conformations of the rhodopsin-Gi signaling complex.
Authors: Filip Pamula / Oliver Tejero / Jonas Mühle / Ralf Thoma / Gebhard F X Schertler / Jacopo Marino / Ching-Ju Tsai /
Abstract: Antibody Fab fragments are widely used protein binders that assist in structural studies of G-protein-coupled receptor (GPCR) signaling complexes. Expanding the repertoire of such binders to target ...Antibody Fab fragments are widely used protein binders that assist in structural studies of G-protein-coupled receptor (GPCR) signaling complexes. Expanding the repertoire of such binders to target distinct components of the signaling complex offers opportunities to probe conformational regulation and dynamics. Here, we report the biochemical and cryo-EM characterization of two Fab fragments, Fab79 and Fab13, raised against the rhodopsin-Gαiβγ complex. Fab79 binds to the flexible α-helical domain (AHD) of the Gαi subunit and prevents complex dissociation in the presence of the nonhydrolyzable GTP analog, GTPγS, likely by hindering AHD closure, a step necessary for complex dissociation. In contrast, Fab13 binds rigidly to Gβ without directly contacting Gα or the receptor. These findings show that Fab79 and Fab13 reveal functionally relevant conformational states of G-protein activation and serve as practical tools to stabilize or modulate GPCR signaling complexes.
History
DepositionMay 11, 2023-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17345.png

Downloads & links

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Map

FileDownload / File: emd_17345.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 380 pix.
= 324.52 Å		0.85 Å/pix.
x 380 pix.
= 324.52 Å		0.85 Å/pix.
x 380 pix.
= 324.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.854 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055
Minimum - Maximum-0.016117224 - 0.032009635
Average (Standard dev.)0.000069978196 (±0.00094272156)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 324.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17345_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_17345_half_map_2.map
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Sample components

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Entire : Rhodopsin-Gi-scFv16-Fab79 complex

EntireName: Rhodopsin-Gi-scFv16-Fab79 complex
Components
  • Complex: Rhodopsin-Gi-scFv16-Fab79 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: single-chain Fv scFv16
      • Protein or peptide: single-chain Fv scFv16
    • Complex: Immunoglobin G heavy chain FAB fragment and Immunoglobin G light chain
      • Protein or peptide: Immunoglobin G heavy chain FAB fragment
      • Protein or peptide: Immunoglobin G light chain

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Supramolecule #1: Rhodopsin-Gi-scFv16-Fab79 complex

SupramoleculeName: Rhodopsin-Gi-scFv16-Fab79 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: bovine rhodopsin N2C/M257Y/D282C
Molecular weightTheoretical: 195 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: single-chain Fv scFv16

SupramoleculeName: single-chain Fv scFv16 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #6: Immunoglobin G heavy chain FAB fragment and Immunoglobin G light chain

SupramoleculeName: Immunoglobin G heavy chain FAB fragment and Immunoglobin G light chain
type: complex / ID: 6 / Parent: 1 / Macromolecule list: #6-#7
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: single-chain Fv scFv16

MacromoleculeName: single-chain Fv scFv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.784896 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KAAAHHHHHH HH

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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: 27.971973 KDa
SequenceString: MNFVLSLIFL ALILKGVQCE VQLVESGGGL VKPGGSLKLS CAASGFTFSS YAMSWVRQTP EKRLEWVATI SSRGLYTYFP DSMKGRFTI SRDNAKNTLS LQMSSLRSED TAMYYCLRGG GYDADYWGQG TTLTVSSAKT TAPSVYPLAP VCGDTTGSSV T LGCLVKGY ...String:
MNFVLSLIFL ALILKGVQCE VQLVESGGGL VKPGGSLKLS CAASGFTFSS YAMSWVRQTP EKRLEWVATI SSRGLYTYFP DSMKGRFTI SRDNAKNTLS LQMSSLRSED TAMYYCLRGG GYDADYWGQG TTLTVSSAKT TAPSVYPLAP VCGDTTGSSV T LGCLVKGY FPEPVTLTWN SGSLSSGVHT FPAVLQSDLY TLSSSVTVTS STWPSQSITC NVAHPASSTK VDKKIEPRGP TI KPCPPCK CPAPNLLGGP SVFIF

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Macromolecule #7: Immunoglobin G light chain

MacromoleculeName: Immunoglobin G light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.37258 KDa
SequenceString: MMSPAQFLFL LVLWIRETNG DVVMTQTPLT LSVTIGQPAS ISCKSSQSLL DSDGETSLNW LLQRPGQSPK RLIYLVSKLD SGVPDRFTG SGSGTDFTLK ISRVEAADLG VYYCWQGTHF PLTFGAGTKL ELKRADAAPT VSIFPPSSEQ LTSGGASVVC F LNNFYPKD ...String:
MMSPAQFLFL LVLWIRETNG DVVMTQTPLT LSVTIGQPAS ISCKSSQSLL DSDGETSLNW LLQRPGQSPK RLIYLVSKLD SGVPDRFTG SGSGTDFTLK ISRVEAADLG VYYCWQGTHF PLTFGAGTKL ELKRADAAPT VSIFPPSSEQ LTSGGASVVC F LNNFYPKD INVKWKIDGS ERQNGVLNSW TDQDSKDSTY SMSSTLTLTK DEYERHNSYT CEATHKTSTS PIVKSFNRNE C

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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

Concentration0.7 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
DetailsMonodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
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: 7026029
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 118000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.13)
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChainDetails

6qno

chain_id: R, residue_range: 1-322, source_name: PDB, initial_model_type: experimental model

6qno

chain_id: A, residue_range: 1-42, source_name: PDB, initial_model_type: experimental model

6qno

chain_id: A, residue_range: 181-354, source_name: PDB, initial_model_type: experimental model
chain_id: A, residue_range: 43-180, source_name: AlphaFold, initial_model_type: in silico model

6qno

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

6qno

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

6crk

chain_id: S, source_name: PDB, initial_model_type: experimental modelchain D in 6CRK.pdb
chain_id: H, source_name: AlphaFold, initial_model_type: in silico model
chain_id: L, source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 295 / Target criteria: cross-correlation coefficient
Output model

PDB-8p15:
Cryo-EM structure of Rhodopsin-Gi bound with antibody fragments scFv16 and Fab79, conformation 2

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