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- PDB-7xwo: Neurokinin A bound to active human neurokinin 2 receptor in compl... -

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Basic information

Entry
Database: PDB / ID: 7xwo
TitleNeurokinin A bound to active human neurokinin 2 receptor in complex with G324
Components
  • (Guanine nucleotide-binding protein ...) x 2
  • G324
  • HIS-LYS-THR-ASP-SER-PHE-VAL-GLY-LEU-MET-NH2
  • Soluble cytochrome b562,Substance-K receptor
  • scFv
KeywordsMEMBRANE PROTEIN / Tachykinin receptor 2 / Neurokinin A
Function / homology
Function and homology information


substance K receptor activity / prolactin secretion / intestine smooth muscle contraction / tachykinin receptor activity / positive regulation of flagellated sperm motility / Tachykinin receptors bind tachykinins / positive regulation of uterine smooth muscle contraction / negative regulation of luteinizing hormone secretion / positive regulation of monoatomic ion transport / operant conditioning ...substance K receptor activity / prolactin secretion / intestine smooth muscle contraction / tachykinin receptor activity / positive regulation of flagellated sperm motility / Tachykinin receptors bind tachykinins / positive regulation of uterine smooth muscle contraction / negative regulation of luteinizing hormone secretion / positive regulation of monoatomic ion transport / operant conditioning / tachykinin receptor signaling pathway / sperm head / positive regulation of acetylcholine secretion, neurotransmission / positive regulation of smooth muscle contraction / positive regulation of vascular permeability / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / 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 / photoreceptor outer segment membrane / G alpha (s) signalling events / G alpha (q) signalling events / spectrin binding / 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 / alkylglycerophosphoethanolamine phosphodiesterase activity / response to electrical stimulus / photoreceptor outer segment / sperm flagellum / sperm midpiece / cardiac muscle cell apoptotic process / photoreceptor inner segment / muscle contraction / electron transport chain / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / retina development in camera-type eye / positive regulation of cytosolic calcium ion concentration / cell body / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / cellular response to hypoxia / G alpha (q) signalling events / periplasmic space / electron transfer activity / cell population proliferation / G protein-coupled receptor signaling pathway / iron ion binding / GTPase activity / heme binding / synapse / dendrite / protein-containing complex binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Neurokinin NK2 receptor / Neurokinin receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein, gamma subunit ...Neurokinin NK2 receptor / Neurokinin receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 / Mainly Beta
Similarity search - Domain/homology
Soluble cytochrome b562 / Substance-K receptor / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSun, W.J. / Yuan, Q.N. / Zhang, H.H. / Yang, F. / Ling, S.L. / Lv, P. / Eric, X. / Tian, C.L. / Yin, W.C. / Shi, P.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Cell Discov / Year: 2022
Title: Structural insights into the activation of neurokinin 2 receptor by neurokinin A.
Authors: Wenjing Sun / Qingning Yuan / Huanhuan Zhang / Fan Yang / Shenglong Ling / Yifan Luo / Pei Lv / H Eric Xu / Changlin Tian / Wanchao Yin / Pan Shi /
History
DepositionMay 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Soluble cytochrome b562,Substance-K receptor
C: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
E: scFv
F: G324
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
D: HIS-LYS-THR-ASP-SER-PHE-VAL-GLY-LEU-MET-NH2


Theoretical massNumber of molelcules
Total (without water)178,3646
Polymers178,3646
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules BF

#1: Protein Soluble cytochrome b562,Substance-K receptor / Cytochrome b-562 / SKR / NK-2 receptor / NK-2R / Neurokinin A receptor / Tachykinin receptor 2


Mass: 57108.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: cybC, TACR2, NK2R, NKNAR, TAC2R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7, UniProt: P21452
#4: Protein G324


Mass: 41710.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Guanine nucleotide-binding protein ... , 2 types, 2 molecules CG

#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37784.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnb1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54311
#5: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63212

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Antibody / Protein/peptide , 2 types, 2 molecules ED

#3: Antibody scFv


Mass: 32692.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm)
#6: Protein/peptide HIS-LYS-THR-ASP-SER-PHE-VAL-GLY-LEU-MET-NH2


Mass: 1207.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The NKA-bound neurokinin 2 receptor and Gq heterotrimer complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapien (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 610257 / Symmetry type: POINT
RefinementCross valid method: NONE / Stereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00698914
ELECTRON MICROSCOPYf_angle_d0.829812099
ELECTRON MICROSCOPYf_chiral_restr0.05631373
ELECTRON MICROSCOPYf_plane_restr0.00771537
ELECTRON MICROSCOPYf_dihedral_angle_d3.90535256

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