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- EMDB-61427: cryo-EM structure of Neuromedin B receptor in complex with PD168368 -

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Basic information

Entry
Database: EMDB / ID: EMD-61427
Titlecryo-EM structure of Neuromedin B receptor in complex with PD168368
Map data
Sample
  • Complex: Neuromedin B Receptor/de novo design fusion protein
    • Protein or peptide: Neuromedin-B receptor,de novo design protein
  • Ligand: (2~{S})-3-(1~{H}-indol-3-yl)-2-methyl-2-[(4-nitrophenyl)carbamoylamino]-~{N}-[(1-pyridin-2-ylcyclohexyl)methyl]propanamide
KeywordsGPCR / inactive-state / de novo protein / MEMBRANE 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGao K / Zhang X / Liu X
Funding support China, 1 items
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, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61427.png

Downloads & links

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Map

FileDownload / File: emd_61427.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.022626 - 4.8687572
Average (Standard dev.)-0.0013855952 (±0.058704402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61427_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61427_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Neuromedin B Receptor/de novo design fusion protein

EntireName: Neuromedin B Receptor/de novo design fusion protein
Components
  • Complex: Neuromedin B Receptor/de novo design fusion protein
    • Protein or peptide: Neuromedin-B receptor,de novo design protein
  • Ligand: (2~{S})-3-(1~{H}-indol-3-yl)-2-methyl-2-[(4-nitrophenyl)carbamoylamino]-~{N}-[(1-pyridin-2-ylcyclohexyl)methyl]propanamide

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Supramolecule #1: Neuromedin B Receptor/de novo design fusion protein

SupramoleculeName: Neuromedin B Receptor/de novo design fusion protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neuromedin-B receptor,de novo design protein

MacromoleculeName: Neuromedin-B receptor,de novo design protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.911129 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDAMPS KSLSNLSVTT GANESGSVPE GWERDFLPAS DGTTTELVIR CVIPSLYLLI ITVGLLGNIM LVKIFITNSA MRSVPNIFI SNLAAGDLLL LLTCVPVDAS RYFFDEWMFG KVGCKLIPVI QLTSVGVSVW TLTALSADRY RAIVNPMDMQ T SGALLRTC ...String:
DYKDDDAMPS KSLSNLSVTT GANESGSVPE GWERDFLPAS DGTTTELVIR CVIPSLYLLI ITVGLLGNIM LVKIFITNSA MRSVPNIFI SNLAAGDLLL LLTCVPVDAS RYFFDEWMFG KVGCKLIPVI QLTSVGVSVW TLTALSADRY RAIVNPMDMQ T SGALLRTC VKAMGIWVVS VLLAVPEAVF SEVARISSLD NSSFTACIPY PQTDELHPKI HSVLIFLVYF LIPLAIISIY YY HIAKHLK EKAKAGAEIA AHPDAFLFLL FAAFGVVLTG DPEDRALWAE LLALVERAAP GIARALAAAY RAAEEAYRAG GPV AGFRAG ILGACAGVDA ETRLPLTARI VDLLRTIRAL RDDEAALRAL VDALGAELRA LLAPVAADAE ELDALLARLA DLAL VALRE LAKLSESEMD AFIADLTAAV EAMAKQMETR KRLAKIVLVF VGCFIFCWFP NHILYMYRSF NYNEIDPSLG HMIVT LVAR VLSFGNSCVN PFALYLLSES FRRHFNSQLC HHHHHH

UniProtKB: Neuromedin-B receptor, Neuromedin-B receptor

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Macromolecule #2: (2~{S})-3-(1~{H}-indol-3-yl)-2-methyl-2-[(4-nitrophenyl)carbamoyl...

MacromoleculeName: (2~{S})-3-(1~{H}-indol-3-yl)-2-methyl-2-[(4-nitrophenyl)carbamoylamino]-~{N}-[(1-pyridin-2-ylcyclohexyl)methyl]propanamide
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1D63
Molecular weightTheoretical: 554.639 Da

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 149635
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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