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Yorodumi- EMDB-33497: Neurokinin A bound to active human neurokinin 2 receptor in compl... -
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-Basic information
Entry | Database: EMDB / ID: EMD-33497 | |||||||||
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Title | Neurokinin A bound to active human neurokinin 2 receptor in complex with G324 | |||||||||
Map data | Neurokinin A bound to active human neurokinin 2 receptor in complex with G324. | |||||||||
Sample |
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Keywords | Tachykinin receptor 2 / Neurokinin A / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information substance K receptor activity / prolactin secretion / intestine smooth muscle contraction / tachykinin receptor activity / Tachykinin receptors bind tachykinins / negative regulation of luteinizing hormone secretion / positive regulation of flagellated sperm motility / positive regulation of monoatomic ion transport / positive regulation of uterine smooth muscle contraction / tachykinin receptor signaling pathway ...substance K receptor activity / prolactin secretion / intestine smooth muscle contraction / tachykinin receptor activity / Tachykinin receptors bind tachykinins / negative regulation of luteinizing hormone secretion / positive regulation of flagellated sperm motility / positive regulation of monoatomic ion transport / positive regulation of uterine smooth muscle contraction / tachykinin receptor signaling pathway / operant conditioning / sperm head / positive regulation of acetylcholine secretion, neurotransmission / positive regulation of smooth muscle contraction / 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 / positive regulation of vascular permeability / Activation of G protein gated Potassium channels / Ca2+ pathway / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / 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 / alkylglycerophosphoethanolamine phosphodiesterase activity / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / 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 / cardiac muscle cell apoptotic process / sperm midpiece / photoreceptor inner segment / electron transport chain / muscle contraction / 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 / retina development in camera-type eye / GTPase binding / 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 sapien (human) / Homo sapiens (human) / Rattus norvegicus (Norway rat) / Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Sun WJ / Yuan QN / Zhang HH / Yang F / Ling SL / Lv P / Eric X / Tian CL / Yin WC / Shi P | |||||||||
Funding support | China, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33497.map.gz | 89.2 MB | EMDB map data format | |
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Header (meta data) | emd-33497-v30.xml emd-33497.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
Images | emd_33497.png | 91.4 KB | ||
Filedesc metadata | emd-33497.cif.gz | 6.5 KB | ||
Others | emd_33497_half_map_1.map.gz emd_33497_half_map_2.map.gz | 80.8 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33497 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33497 | HTTPS FTP |
-Related structure data
Related structure data | 7xwoMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33497.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Neurokinin A bound to active human neurokinin 2 receptor in complex with G324. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.824 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Neurokinin A bound to active human neurokinin 2...
File | emd_33497_half_map_1.map | ||||||||||||
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Annotation | Neurokinin A bound to active human neurokinin 2 receptor in complex with G324. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Neurokinin A bound to active human neurokinin 2...
File | emd_33497_half_map_2.map | ||||||||||||
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Annotation | Neurokinin A bound to active human neurokinin 2 receptor in complex with G324. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The NKA-bound neurokinin 2 receptor and Gq heterotrimer complex
Entire | Name: The NKA-bound neurokinin 2 receptor and Gq heterotrimer complex |
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Components |
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-Supramolecule #1: The NKA-bound neurokinin 2 receptor and Gq heterotrimer complex
Supramolecule | Name: The NKA-bound neurokinin 2 receptor and Gq heterotrimer complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapien (human) |
-Macromolecule #1: Soluble cytochrome b562,Substance-K receptor
Macromolecule | Name: Soluble cytochrome b562,Substance-K receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 57.108215 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKTIIALSYI FCLVFADYKD DDDAKLQTMH HHHHHHHHHE NLYFQGGTAD LEDNWETLND NLKVIEKADN AAQVKDALTK MRAAALDAQ KATPPKLEDK SPDSPEMKDF RHGFDILVGQ IDDALKLANE GKVKEAQAAA EQLKTTRNAY IQKYLMGTCD I VTEANISS ...String: MKTIIALSYI FCLVFADYKD DDDAKLQTMH HHHHHHHHHE NLYFQGGTAD LEDNWETLND NLKVIEKADN AAQVKDALTK MRAAALDAQ KATPPKLEDK SPDSPEMKDF RHGFDILVGQ IDDALKLANE GKVKEAQAAA EQLKTTRNAY IQKYLMGTCD I VTEANISS GPESNTTGIT AFSMPSWQLA LWATAYLALV LVAVTGNAIV IWIILAHRRM RTVTNYFIVN LALADLCMAA FN AAFNFVY ASHNIWYFGR AFCYFQNLFP ITAMFVSIYS MTAIAADRYM AIVHPFQPRL SAPSTKAVIA GIWLVALALA SPQ CFYSTV TMDQGATKCV VAWPEDSGGK TLLLYHLVVI ALIYFLPLAV MFVAYSVIGL TLWRRAVPGH QAHGANLRHL QAMK KFVKT MVLVVLTFAI CWLPYHLYFI LGSFQEDIYC HKFIQQVYLA LFWLAMSSTM YNPIIYCCLN HRFRSGFRLA FRCCP WVTP TKEDKLELTP TTSLSKLVEK Y UniProtKB: Soluble cytochrome b562, Substance-K receptor |
-Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: 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 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 37.784301 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT ...String: GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT TCALWDIETG QQTTTFTGHT GDVMSLSLAP DTRLFVSGAC DASAKLWDVR EGMCRQTFTG HESDINAICF FP NGNAFAT GSDDATCRLF DLRADQELMT YSHDNIICGI TSVSFSKSGR LLLAGYDDFN CNVWDALKAD RAGVLAGHDN RVS CLGVTD DGMAVATGSW DSFLKIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #3: scFv
Macromolecule | Name: scFv / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 32.692473 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAVQ LVESGGGLVQ PGGSRKLSCS ASGFAFSSFG MHWVRQAPEK GLEWVAYIS SGSGTIYYAD TVKGRFTISR DDPKNTLFLQ MTSLRSEDTA MYYCVRSIYY YGSSPFDFWG QGTTLTVSAG G GGSGGGGS ...String: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAVQ LVESGGGLVQ PGGSRKLSCS ASGFAFSSFG MHWVRQAPEK GLEWVAYIS SGSGTIYYAD TVKGRFTISR DDPKNTLFLQ MTSLRSEDTA MYYCVRSIYY YGSSPFDFWG QGTTLTVSAG G GGSGGGGS GGGGSADIVM TQATSSVPVT PGESVSISCR SSKSLLHSNG NTYLYWFLQR PGQSPQLLIY RMSNLASGVP DR FSGSGSG TAFTLTISRL EAEDVGVYYC MQHLEYPLTF GAGTKLELVD ENLYFQGASH HHHHHHH |
-Macromolecule #4: G324
Macromolecule | Name: G324 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.710289 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTSGIFETK FQVDKVNFHM FDVGAQRDER RKWIQCFNDV TAIIFVVDSS DYNRLQEALN DF DSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED YFPEFARYTT PEDATPEPGE DPRVTRAKYF IRKEFVDIST ASG DGRHIC YPHFTCSVDT ENARRIFNDC KDIILQMNLR EYNLV |
-Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: 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 |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 7.861143 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #6: HIS-LYS-THR-ASP-SER-PHE-VAL-GLY-LEU-MET-NH2
Macromolecule | Name: HIS-LYS-THR-ASP-SER-PHE-VAL-GLY-LEU-MET-NH2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.207399 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: HKTDSFVGLM A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 610257 |