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- PDB-9jf4: cryo-EM structure of Neuromedin B receptor in complex with PD168368 -

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Basic information

Entry
Database: PDB / ID: 9jf4
Titlecryo-EM structure of Neuromedin B receptor in complex with PD168368
ComponentsNeuromedin-B receptor,de novo design protein
KeywordsMEMBRANE PROTEIN / GPCR / inactive-state / de novo protein
Function / homology
Function and homology information


sneeze reflex / bombesin receptor activity / positive regulation of respiratory gaseous exchange / positive regulation of osteoclast proliferation / neuropeptide receptor activity / negative regulation of interleukin-6 production / positive regulation of interferon-alpha production / antiviral innate immune response / Peptide ligand-binding receptors / phospholipase C-activating G protein-coupled receptor signaling pathway ...sneeze reflex / bombesin receptor activity / positive regulation of respiratory gaseous exchange / positive regulation of osteoclast proliferation / neuropeptide receptor activity / negative regulation of interleukin-6 production / positive regulation of interferon-alpha production / antiviral innate immune response / Peptide ligand-binding receptors / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / plasma membrane / cytosol
Similarity search - Function
Neuromedin B receptor / Bombesin receptor-like / Serpentine type 7TM GPCR chemoreceptor Srsx / 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)
Similarity search - Domain/homology
: / Neuromedin-B receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGao, K. / Zhang, X. / Liu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81974236 China
CitationJournal: To Be Published
Title: cryo-EM structure of Neuromedin B receptor in complex with PD168368
Authors: Gao, K. / Zhang, X. / Liu, X.
History
DepositionSep 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuromedin-B receptor,de novo design protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4662
Polymers56,9111
Non-polymers5551
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Neuromedin-B receptor,de novo design protein / NMB-R / Epididymis tissue protein Li 185a / Neuromedin-B-preferring bombesin receptor


Mass: 56911.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMBR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28336
#2: Chemical ChemComp-A1D63 / (2~{S})-3-(1~{H}-indol-3-yl)-2-methyl-2-[(4-nitrophenyl)carbamoylamino]-~{N}-[(1-pyridin-2-ylcyclohexyl)methyl]propanamide / PD 168368


Mass: 554.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H34N6O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Neuromedin B Receptor/de novo design fusion protein / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (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

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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: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149635 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0042836
ELECTRON MICROSCOPYf_angle_d0.5473883
ELECTRON MICROSCOPYf_dihedral_angle_d6.406410
ELECTRON MICROSCOPYf_chiral_restr0.036493
ELECTRON MICROSCOPYf_plane_restr0.003474

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