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- EMDB-24570: Substance P bound to active human neurokinin 1 receptor in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-24570
TitleSubstance P bound to active human neurokinin 1 receptor in complex with miniGs399
Map data
Sample
  • Complex: Substance P bound to Neurokinin1 receptor-miniGs399 complex
    • Complex: Substance P
      • Protein or peptide: Substance P
    • Complex: Substance-P receptor
      • Protein or peptide: Substance-P receptor
    • Complex: miniGs399
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1/gamma-2
      • 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: Nanobody 35
      • Protein or peptide: Nanobody 35
KeywordsSubstance P / G protein / GPCR / Neurokinin / Tachykinin / SIGNALING PROTEIN / SIGNALING PROTEIN-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


substance P receptor binding / substance P receptor activity / positive regulation of corticosterone secretion / tachykinin receptor activity / positive regulation of flagellated sperm motility / aggressive behavior / Tachykinin receptors bind tachykinins / sperm ejaculation / positive regulation of uterine smooth muscle contraction / insemination ...substance P receptor binding / substance P receptor activity / positive regulation of corticosterone secretion / tachykinin receptor activity / positive regulation of flagellated sperm motility / aggressive behavior / Tachykinin receptors bind tachykinins / sperm ejaculation / positive regulation of uterine smooth muscle contraction / insemination / positive regulation of synaptic transmission, cholinergic / detection of abiotic stimulus / operant conditioning / positive regulation of lymphocyte proliferation / tachykinin receptor signaling pathway / response to ozone / sperm head / positive regulation of action potential / response to auditory stimulus / positive regulation of acute inflammatory response / positive regulation of blood pressure / smooth muscle contraction involved in micturition / regulation of smooth muscle cell proliferation / positive regulation of vascular permeability / positive regulation of hormone secretion / positive regulation of ossification / regulation of smooth muscle cell migration / positive regulation of leukocyte migration / eating behavior / negative regulation of heart rate / response to pain / positive regulation of vasoconstriction / behavioral response to pain / angiotensin-mediated drinking behavior / associative learning / positive regulation of epithelial cell migration / PKA activation in glucagon signalling / response to electrical stimulus / developmental growth / hair follicle placode formation / neuropeptide signaling pathway / long-term memory / D1 dopamine receptor binding / sperm flagellum / neuronal dense core vesicle / intracellular transport / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / activation of adenylate cyclase activity / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / response to hormone / positive regulation of stress fiber assembly / sperm midpiece / sensory perception of pain / cellular response to glucagon stimulus / regulation of insulin secretion / response to progesterone / adenylate cyclase activator activity / trans-Golgi network membrane / positive regulation of epithelial cell proliferation / positive regulation of synaptic transmission, GABAergic / response to nicotine / negative regulation of inflammatory response to antigenic stimulus / cellular response to nerve growth factor stimulus / bone development / regulation of blood pressure / platelet aggregation / G-protein beta/gamma-subunit complex binding / cognition / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / 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 / sensory perception of smell / 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
Similarity search - Function
Tachykinin family / Tachykinin family / Tachykinin domain / Tachykinin family / Neurokinin NK1 receptor / Neurokinin receptor / Tachykinin/Neurokinin-like, conserved site / Tachykinin family signature. / G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit ...Tachykinin family / Tachykinin family / Tachykinin domain / Tachykinin family / Neurokinin NK1 receptor / Neurokinin receptor / Tachykinin/Neurokinin-like, conserved site / Tachykinin family signature. / G-protein alpha subunit, group S / 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. / 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. / 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
Protachykinin-1 / Substance-P receptor / 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(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHarris JA / Faust B
Funding support United States, Australia, 11 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5OD023048 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127359 United States
National Health and Medical Research Council (NHMRC, Australia)APP1138448 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1196951 Australia
Australian Research Council (ARC)DE170100152 Australia
National Science Foundation (NSF, United States)2034836 United States
Human Frontier Science Program (HFSP)LT000916/2018-L United States
National Institutes of Health/Office of the DirectorS10OD020054 United States
National Institutes of Health/Office of the DirectorS10OD020054 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129541 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Chem Biol / Year: 2022
Title: Selective G protein signaling driven by substance P-neurokinin receptor dynamics.
Authors: Julian A Harris / Bryan Faust / Arisbel B Gondin / Marc André Dämgen / Carl-Mikael Suomivuori / Nicholas A Veldhuis / Yifan Cheng / Ron O Dror / David M Thal / Aashish Manglik /
Abstract: The neuropeptide substance P (SP) is important in pain and inflammation. SP activates the neurokinin-1 receptor (NK1R) to signal via G and G proteins. Neurokinin A also activates NK1R, but leads to ...The neuropeptide substance P (SP) is important in pain and inflammation. SP activates the neurokinin-1 receptor (NK1R) to signal via G and G proteins. Neurokinin A also activates NK1R, but leads to selective G signaling. How two stimuli yield distinct G protein signaling at the same G protein-coupled receptor remains unclear. We determined cryogenic-electron microscopy structures of active NK1R bound to SP or the G-biased peptide SP6-11. Peptide interactions deep within NK1R are critical for receptor activation. Conversely, interactions between SP and NK1R extracellular loops are required for potent G signaling but not G signaling. Molecular dynamics simulations showed that these superficial contacts restrict SP flexibility. SP6-11, which lacks these interactions, is dynamic while bound to NK1R. Structural dynamics of NK1R agonists therefore depend on interactions with the receptor extracellular loops and regulate G protein signaling selectivity. Similar interactions between other neuropeptides and their cognate receptors may tune intracellular signaling.
History
DepositionJul 27, 2021-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rmh
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24570.png

Downloads & links

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Map

FileDownload / File: emd_24570.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-6.399435 - 13.381161000000001
Average (Standard dev.)-0.0017810302 (±0.3139547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z275.200275.200275.200
α/β/γ90.00090.00090.000
start NX/NY/NZ799196
NX/NY/NZ149138117
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-6.39913.381-0.002

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Supplemental data

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Additional map: #1

Fileemd_24570_additional_1.map
Projections & Slices
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Half map: #1

Fileemd_24570_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_24570_half_map_2.map
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Sample components

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Entire : Substance P bound to Neurokinin1 receptor-miniGs399 complex

EntireName: Substance P bound to Neurokinin1 receptor-miniGs399 complex
Components
  • Complex: Substance P bound to Neurokinin1 receptor-miniGs399 complex
    • Complex: Substance P
      • Protein or peptide: Substance P
    • Complex: Substance-P receptor
      • Protein or peptide: Substance-P receptor
    • Complex: miniGs399
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1/gamma-2
      • 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: Nanobody 35
      • Protein or peptide: Nanobody 35

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Supramolecule #1: Substance P bound to Neurokinin1 receptor-miniGs399 complex

SupramoleculeName: Substance P bound to Neurokinin1 receptor-miniGs399 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Substance P

SupramoleculeName: Substance P / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

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Supramolecule #3: Substance-P receptor

SupramoleculeName: Substance-P receptor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: miniGs399

SupramoleculeName: miniGs399 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: 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/gamma-2
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: Nanobody 35

SupramoleculeName: Nanobody 35 / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lama glama (llama)

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Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.907684 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NSKTEDQRNE EKAQREANKK IEKQLQKDKQ VYRATHRLLL LGADNSGKST IVKQMRILHG GSGGSGGTSG IFETKFQVDK VNFHMFDVG GQRDERRKWI QCFNDVTAII FVVDSSDYNR LQEALNLFKS IWNNRWLRTI SVILFLNKQD LLAEKVLAGK S KIEDYFPE ...String:
NSKTEDQRNE EKAQREANKK IEKQLQKDKQ VYRATHRLLL LGADNSGKST IVKQMRILHG GSGGSGGTSG IFETKFQVDK VNFHMFDVG GQRDERRKWI QCFNDVTAII FVVDSSDYNR LQEALNLFKS IWNNRWLRTI SVILFLNKQD LLAEKVLAGK S KIEDYFPE FARYTTPEDA TPEPGEDPRV TRAKYFIRDE FLRISTASGD GRHYCYPHFT CAVDTENARR IFNDCRDIIQ RM HLRQYEL L

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

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Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.786566 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHLEV LFQGPEDQVD PRLIDGKGSS GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIY AMHWGTDSRL LVSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR E GNVRVSRE ...String:
MHHHHHHLEV LFQGPEDQVD PRLIDGKGSS GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIY AMHWGTDSRL LVSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR E GNVRVSRE LAGHTGYLSC CRFLDDNQIV TSSGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KL WDVREGM CRQTFTGHES DINAICFFPN GNAFATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYD DFNCNV WDALKADRAG VLAGHDNRVS CLGVTDDGMA VATGSWDSFL KIWN

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

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.56375 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFC

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

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Macromolecule #4: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.398067 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSSG SEDQVDPRLI DGK

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Macromolecule #5: Substance-P receptor

MacromoleculeName: Substance-P receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.542867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDASI DMDNVLPVDS DLSPNISTNT SEPNQFVQPA WQIVLWAAAY TVIVVTSVVG NVVVMWIILA HKRMRTVTNY FLVNLAFAE ASMAAFNTVV NFTYAVHNEW YYGLFYCKFH NFFPIAAVFA SIYSMTAVAF DRYMAIIHPL QPRLSATATK V VICVIWVL ...String:
DYKDDDDASI DMDNVLPVDS DLSPNISTNT SEPNQFVQPA WQIVLWAAAY TVIVVTSVVG NVVVMWIILA HKRMRTVTNY FLVNLAFAE ASMAAFNTVV NFTYAVHNEW YYGLFYCKFH NFFPIAAVFA SIYSMTAVAF DRYMAIIHPL QPRLSATATK V VICVIWVL ALLLAFPQGY YSTTETMPSR VVCMIEWPEH PNKIYEKVYH ICVTVLIYFL PLLVIGYAYT VVGITLWASE IP GDSSDRY HEQVSAKRKV VKMMIVVVCT FAICWLPFHI FFLLPYINPD LYLKKFIQQV YLAIMWLAMS STMYNPIIYC CLN DRFRLG FKHAFRCCPF ISAGDYEGLE MKSTRYLQTQ GSVYKVSRLE TTISTVVGAH EEEPEDGPKA TPSSLDLTSN CSSR SDSKT MTESFSFSSN VLS

UniProtKB: Substance-P receptor

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Macromolecule #6: Substance P

MacromoleculeName: Substance P / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.348637 KDa
SequenceString:
RPKPQQFFGL M(NH2)

UniProtKB: Protachykinin-1

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3670 / Average exposure time: 1.52 sec. / Average electron dose: 49.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4865341
Startup modelType of model: OTHER / Details: From Ab initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 288659
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM
Final 3D classificationNumber classes: 4 / Software - Name: RELION

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Atomic model buiding 1

Initial modelPDB ID:

6hlp


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7rmh:
Substance P bound to active human neurokinin 1 receptor in complex with miniGs399

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