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Yorodumi- PDB-7xwo: Neurokinin A bound to active human neurokinin 2 receptor in compl... -
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-Basic information
Entry | Database: PDB / ID: 7xwo | ||||||
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Title | Neurokinin A bound to active human neurokinin 2 receptor in complex with G324 | ||||||
Components |
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Keywords | MEMBRANE 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 / Tachykinin receptors bind tachykinins / positive regulation of flagellated sperm motility / positive regulation of monoatomic ion transport / positive regulation of uterine smooth muscle contraction / tachykinin receptor signaling pathway / negative regulation of luteinizing hormone secretion ...substance K receptor activity / prolactin secretion / intestine smooth muscle contraction / tachykinin receptor activity / Tachykinin receptors bind tachykinins / positive regulation of flagellated sperm motility / positive regulation of monoatomic ion transport / positive regulation of uterine smooth muscle contraction / tachykinin receptor signaling pathway / negative regulation of luteinizing hormone secretion / operant conditioning / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / 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 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / alkylglycerophosphoethanolamine phosphodiesterase activity / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / 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 / spectrin binding / Vasopressin regulates renal water homeostasis via Aquaporins / photoreceptor outer segment / sperm flagellum / response to electrical stimulus / sperm midpiece / cardiac muscle cell apoptotic process / photoreceptor inner segment / muscle contraction / electron transport chain / cellular response to catecholamine stimulus / sensory perception of taste / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / cell body / positive regulation of cytosolic calcium ion concentration / cellular response to hypoxia / G alpha (q) signalling events / cell population proliferation / periplasmic space / electron transfer activity / iron ion binding / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / heme binding / protein-containing complex binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Sun, 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
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xwo.cif.gz | 222.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xwo.ent.gz | 164 KB | Display | PDB format |
PDBx/mmJSON format | 7xwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xwo_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7xwo_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7xwo_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 7xwo_validation.cif.gz | 61.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/7xwo ftp://data.pdbj.org/pub/pdb/validation_reports/xw/7xwo | HTTPS FTP |
-Related structure data
Related structure data | 33497MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules BF
#1: Protein | 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 |
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#4: Protein | 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) |
-Guanine nucleotide-binding protein ... , 2 types, 2 molecules CG
#2: Protein | 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 |
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#5: Protein | Mass: 7861.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63212 |
-Antibody / Protein/peptide , 2 types, 2 molecules ED
#3: Antibody | 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) |
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#6: Protein/peptide | 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) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The NKA-bound neurokinin 2 receptor and Gq heterotrimer complex Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapien (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 610257 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE / Stereochemistry target values: CDL v1.2 | ||||||||||||||||||||||||
Refine LS restraints |
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