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- EMDB-24569: Substance P bound to active human neurokinin 1 receptor in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-24569
TitleSubstance P bound to active human neurokinin 1 receptor in complex with miniGs/q70
Map data
Sample
  • Complex: Substance P bound to Neurokinin 1 receptor-miniGs/q70 complex
    • Complex: Substance P
      • Protein or peptide: Substance P
    • Complex: Substance-P receptor
      • Protein or peptide: Substance-P receptor
    • Complex: Guanine nucleotide-binding protein G(s)/G(q) subunit alpha hybrid
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, with certain residues mutated to match Guanine nucleotide-binding protein G(q) subunit
    • 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 35Single-domain antibody
      • Protein or peptide: Nanobody 35Single-domain antibody
Function / homology
Function and homology information


substance P receptor binding / substance P receptor activity / insemination / tachykinin receptor activity / positive regulation of flagellated sperm motility / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of uterine smooth muscle contraction / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic ...substance P receptor binding / substance P receptor activity / insemination / tachykinin receptor activity / positive regulation of flagellated sperm motility / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of uterine smooth muscle contraction / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic / operant conditioning / sperm head / sperm ejaculation / positive regulation of lymphocyte proliferation / tachykinin receptor signaling pathway / response to ozone / response to auditory stimulus / positive regulation of action potential / smooth muscle contraction involved in micturition / positive regulation of blood pressure / regulation of smooth muscle cell proliferation / positive regulation of hormone secretion / positive regulation of vascular permeability / positive regulation of ossification / regulation of smooth muscle cell migration / positive regulation of leukocyte migration / response to pain / eating behavior / positive regulation of epithelial cell migration / behavioral response to pain / angiotensin-mediated drinking behavior / PKA activation in glucagon signalling / associative learning / hair follicle placode formation / intracellular transport / D1 dopamine receptor binding / developmental growth / neuropeptide signaling pathway / long-term memory / sperm flagellum / Hedgehog 'off' state / positive regulation of cAMP-mediated signaling / response to electrical stimulus / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of vasoconstriction / sensory perception of pain / positive regulation of stress fiber assembly / sperm midpiece / activation of adenylate cyclase activity / adenylate cyclase activator activity / cellular response to nerve growth factor stimulus / trans-Golgi network membrane / response to progesterone / response to nicotine / positive regulation of epithelial cell proliferation / positive regulation of synaptic transmission, GABAergic / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / bone development / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / platelet aggregation / cognition / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of GTPase activity / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / sensory perception of smell
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 / G-alpha domain profile. ...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 / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / 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 / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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: 3.0 Å
AuthorsHarris JA / Faust B / Gondin AB / Daemgen MA / Suomivuori CM / Veldhuis NA / Cheng Y / Dror RO / Thal D / Manglik A
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-
UpdateJan 5, 2022-
Current statusJan 5, 2022Processing 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-7rmg
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24569.png

Downloads & links

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Map

FileDownload / File: emd_24569.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-5.802195 - 13.7705555
Average (Standard dev.)0.0036118282 (±0.4116517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 240.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8350.8350.835
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z240.480240.480240.480
α/β/γ90.00090.00090.000
start NX/NY/NZ799196
NX/NY/NZ149138117
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-5.80213.7710.004

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Supplemental data

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Additional map: #1

Fileemd_24569_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_24569_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24569_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Substance P bound to Neurokinin 1 receptor-miniGs/q70 complex

EntireName: Substance P bound to Neurokinin 1 receptor-miniGs/q70 complex
Components
  • Complex: Substance P bound to Neurokinin 1 receptor-miniGs/q70 complex
    • Complex: Substance P
      • Protein or peptide: Substance P
    • Complex: Substance-P receptor
      • Protein or peptide: Substance-P receptor
    • Complex: Guanine nucleotide-binding protein G(s)/G(q) subunit alpha hybrid
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, with certain residues mutated to match Guanine nucleotide-binding protein G(q) subunit
    • 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 35Single-domain antibody
      • Protein or peptide: Nanobody 35Single-domain antibody

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Supramolecule #1: Substance P bound to Neurokinin 1 receptor-miniGs/q70 complex

SupramoleculeName: Substance P bound to Neurokinin 1 receptor-miniGs/q70 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: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Substance-P receptor

SupramoleculeName: Substance-P receptor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: Guanine nucleotide-binding protein G(s)/G(q) subunit alpha hybrid

SupramoleculeName: Guanine nucleotide-binding protein G(s)/G(q) subunit alpha hybrid
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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: #4-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #6: Nanobody 35

SupramoleculeName: Nanobody 35 / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, with certain residues mutated to match Guanine nucleotide-binding protein G(q) subunit
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.450961 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GIEKQLQKDK QVYRATHRLL LLGADNSGKS TIVKQMRILH GGSGGSGGTS GIFETKFQVD KVNFHMFDVG GQRDERRKWI QCFNDVTAI IFVVDSSDYN RLQEALNDFK SIWNNRWLRT ISVILFLNKQ DLLAEKVLAG KSKIEDYFPE FARYTTPEDA T PEPGEDPR ...String:
GIEKQLQKDK QVYRATHRLL LLGADNSGKS TIVKQMRILH GGSGGSGGTS GIFETKFQVD KVNFHMFDVG GQRDERRKWI QCFNDVTAI IFVVDSSDYN RLQEALNDFK SIWNNRWLRT ISVILFLNKQ DLLAEKVLAG KSKIEDYFPE FARYTTPEDA T PEPGEDPR VTRAKYFIRD EFLRISTASG DGRHYCYPHF TCAVDTENAR RIFNDCKDII LQMNLREYNL V

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Macromolecule #2: Substance-P receptor

MacromoleculeName: Substance-P receptor / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: Substance P

MacromoleculeName: Substance P / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.348637 KDa
SequenceString:
RPKPQQFFGL M(NH2)

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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: 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

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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: 7.56375 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFC

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Macromolecule #6: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 6 / 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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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 5.9 sec. / Average electron dose: 67.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6945760
CTF correctionSoftware - Name: cryoSPARC / Software - details: Patch CTF
Startup modelType of model: OTHER / Details: From Ab initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 122220

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Atomic model buiding 1

Initial modelPDB ID:

6hlp

Output model

PDB-7rmg:
Substance P bound to active human neurokinin 1 receptor in complex with miniGs/q70

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