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- EMDB-64915: Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi... -

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Entry
Database: EMDB / ID: EMD-64915
TitleCryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the GDP-bound, AHD-closed C state 1, plunge-frozen 15 seconds after GDP addition
Map data
Sample
  • Complex: JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-Gi1 complex in the GDP-bound, AHD-closed C state 1 with scFv16, plunge-frozen 15 seconds after GDP addition
    • Complex: JMV449-bound human neurotensin receptor type 1
      • Protein or peptide: Neurotensin receptor type 1
      • Protein or peptide: JMV449
    • Complex: GDP-bound heterotrimeric Gi1 protein
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: scFv16
      • Protein or peptide: scFv16
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsGPCR / NTSR1 / neurotensin / G-protein / membrane protein
Function / homology
Function and homology information


G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / positive regulation of locomotion / regulation of inositol trisphosphate biosynthetic process / positive regulation of gamma-aminobutyric acid secretion / D-aspartate import across plasma membrane / positive regulation of arachidonate secretion / L-glutamate import across plasma membrane / vocalization behavior ...G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / positive regulation of locomotion / regulation of inositol trisphosphate biosynthetic process / positive regulation of gamma-aminobutyric acid secretion / D-aspartate import across plasma membrane / positive regulation of arachidonate secretion / L-glutamate import across plasma membrane / vocalization behavior / regulation of behavioral fear response / cAMP biosynthetic process / regulation of respiratory gaseous exchange / positive regulation of inhibitory postsynaptic potential / negative regulation of systemic arterial blood pressure / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of glutamate secretion / response to food / regulation of membrane depolarization / response to lipid / temperature homeostasis / positive regulation of inositol phosphate biosynthetic process / detection of temperature stimulus involved in sensory perception of pain / response to stress / conditioned place preference / 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 / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / cellular response to forskolin / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / regulation of mitotic spindle organization / chemokine-mediated signaling pathway / dendritic shaft / adult locomotory behavior / Regulation of insulin secretion / neuropeptide signaling pathway / response to prostaglandin E / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / response to peptide hormone / G protein-coupled receptor activity / cytoplasmic side of plasma membrane / centriolar satellite / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / terminal bouton / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G beta:gamma signalling through BTK / photoreceptor disc membrane / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / GDP binding / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / G alpha (12/13) signalling events / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / extracellular vesicle / sensory perception of taste / sperm principal piece / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / retina development in camera-type eye / GTPase binding / fibroblast proliferation / G protein activity / midbody
Similarity search - Function
Neurotensin receptor / Neurotensin type 1 receptor / G-protein alpha subunit, group I / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. ...Neurotensin receptor / Neurotensin type 1 receptor / G-protein alpha subunit, group I / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / 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
Neurotensin receptor type 1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / 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 speciesHomo sapiens (human) / synthetic construct (others) / Mus musculus (house mouse)
Methodsingle particle reconstruction / Resolution: 2.85 Å
AuthorsKobayashi K / Matsui TE / Fukuda M / Kawakami K / Yamashita K / Kato HE
Funding support Japan, 7 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25K09525 Japan
Japan Society for the Promotion of Science (JSPS)24H02262 Japan
Japan Society for the Promotion of Science (JSPS)25H01338 Japan
Japan Society for the Promotion of Science (JSPS)24KJ0981 Japan
Japan Society for the Promotion of Science (JSPS)25H02243 Japan
Japan Society for the Promotion of Science (JSPS)24K18060 Japan
Japan Society for the Promotion of Science (JSPS)23KJ0363 Japan
CitationJournal: Nature / Year: 2026
Title: The dynamic basis of G-protein recognition and activation by a GPCR.
Authors: Kazuhiro Kobayashi / Kouki Kawakami / Toshiki E Matsui / Shun Yokoi / Masahiro Fukuda / Tomohiro J Narita / Hiroki Arai / Mai Tambo / Takashi Sumikama / Manae Tatsumi / Keitaro Yamashita / ...Authors: Kazuhiro Kobayashi / Kouki Kawakami / Toshiki E Matsui / Shun Yokoi / Masahiro Fukuda / Tomohiro J Narita / Hiroki Arai / Mai Tambo / Takashi Sumikama / Manae Tatsumi / Keitaro Yamashita / Junki Koyanagi / Mai Kugawa / Hisako Ikeda / Ayumi Sumino / Ayori Mitsutake / Brian K Kobilka / Asuka Inoue / Hideaki E Kato /
Abstract: G-protein-coupled receptor (GPCR) signalling occurs through heterotrimeric G proteins, whose selective activation leads to distinct cellular outcomes. Although more than 200 GPCR-G protein complex ...G-protein-coupled receptor (GPCR) signalling occurs through heterotrimeric G proteins, whose selective activation leads to distinct cellular outcomes. Although more than 200 GPCR-G protein complex structures have been determined, these static snapshots provide limited insight into the dynamics of G-protein association and dissociation. Here we present cryo-electron microscopy structures of human neurotensin receptor type 1 (NTSR1) with minimally modified G and G, showing how the receptor's intracellular surface dynamically rearranges to accommodate each G-protein subtype. Furthermore, time-resolved cryo-electron microscopy analyses of NTSR1-G visualized G-protein dissociation processes on GDP/GTP binding. Characterization of more than 20 intermediates, complemented by mutational and computational analyses, identifies four key mechanistic features. First, GDP/GTP induces G release from both canonical and non-canonical active conformations with distinct kinetics. Second, NTSR1 uses common intracellular rearrangements to recognize different G-protein subtypes and to promote activation of a single subtype. Third, separation from Gβγ involves stepwise remodelling of the Gα switches I-III. Finally, G dissociates from the receptor through a pathway that is distinct from that of G, and the canonical and non-canonical NTSR1-G complexes further diverge in their dissociation trajectories. These findings provide a comprehensive framework for understanding GPCR signalling dynamics and guiding signal-targeted therapeutic development.
History
DepositionJun 4, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64915.png

Downloads & links

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Map

FileDownload / File: emd_64915.map.gz / Format: CCP4 / Size: 6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 116 pix.
= 160.467 Å		1.38 Å/pix.
x 116 pix.
= 160.467 Å		1.38 Å/pix.
x 116 pix.
= 160.467 Å

Surface

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Voxel sizeX=Y=Z: 1.38333 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.308
Minimum - Maximum-0.7321034 - 1.6426203
Average (Standard dev.)-0.006242765 (±0.09415648)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions116116116
Spacing116116116
CellA=B=C: 160.46666 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64915_msk_1.map
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Additional map: #1

Fileemd_64915_additional_1.map
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Half map: #2

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Half map: #1

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Sample components

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Entire : JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-Gi1 complex in...

EntireName: JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-Gi1 complex in the GDP-bound, AHD-closed C state 1 with scFv16, plunge-frozen 15 seconds after GDP addition
Components
  • Complex: JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-Gi1 complex in the GDP-bound, AHD-closed C state 1 with scFv16, plunge-frozen 15 seconds after GDP addition
    • Complex: JMV449-bound human neurotensin receptor type 1
      • Protein or peptide: Neurotensin receptor type 1
      • Protein or peptide: JMV449
    • Complex: GDP-bound heterotrimeric Gi1 protein
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: scFv16
      • Protein or peptide: scFv16
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-Gi1 complex in...

SupramoleculeName: JMV449-bound human Neurotensin Receptor 1 (hNTSR1)-Gi1 complex in the GDP-bound, AHD-closed C state 1 with scFv16, plunge-frozen 15 seconds after GDP addition
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: JMV449-bound human neurotensin receptor type 1

SupramoleculeName: JMV449-bound human neurotensin receptor type 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: GDP-bound heterotrimeric Gi1 protein

SupramoleculeName: GDP-bound heterotrimeric Gi1 protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6

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Macromolecule #1: Neurotensin receptor type 1

MacromoleculeName: Neurotensin receptor type 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.535051 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGQPGNGSAF LLAPNRSHAP DHDVENLYFQ GQRAQAGLEE ALLAPGFGNA SGNASERVLA APSSELDVNT DIYSKVLVTA VYLALFVVG TVGNTVTLFT LARKKSLQSL QSTVHYHLGS LALSDLLTLL LAMPVELYNF IWVHHPWAFG DAGCRGYYFL R DACTYATA ...String:
MGQPGNGSAF LLAPNRSHAP DHDVENLYFQ GQRAQAGLEE ALLAPGFGNA SGNASERVLA APSSELDVNT DIYSKVLVTA VYLALFVVG TVGNTVTLFT LARKKSLQSL QSTVHYHLGS LALSDLLTLL LAMPVELYNF IWVHHPWAFG DAGCRGYYFL R DACTYATA LNVASLSVER YLAICHPFKA KTLMSRSRTK KFISAIWLAS ALLAVPMLFT MGEQNRSADG QHAGGLVCTP TI HTATVKV VIQVNTFMSF IFPMVVISVL NTIIANKLTV MVRQAAEQGQ VCTVGGEHST FSMAIEPGRV QALRHGVRVL RAV VIAFVV CWLPYHVRRL MFCYISDEQW TPFLYDFYHY FYMVTNALFY VSSTINPILY NLVSANFRHI FLATLACLCP VWRR RRKRP AFSRKADSVS SNHTLSSNAT RETLYLEVLF Q

UniProtKB: Neurotensin receptor type 1

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Macromolecule #2: JMV449

MacromoleculeName: JMV449 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 762.979 Da
SequenceString:
KKPYIL

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

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.415031 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGGQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCA TDTKNVQFVF DAVTDVIIKN NLKDCGLF

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

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.418086 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR ...String:
MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR FLDDNQIVTS SGDTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TF TGHESDI NAICFFPNGN AFATGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKA DRAGVL AGHDNRVSCL GVTDDGMAVA TGSWDSFLKI WN

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

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Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #6: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 6 / 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 #7: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6os9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 452691
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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