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- EMDB-20284: Cryo-EM structure of Urocortin 1-bound Corticotropin-releasing fa... -

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Entry
Database: EMDB / ID: EMD-20284
TitleCryo-EM structure of Urocortin 1-bound Corticotropin-releasing factor 1 receptor in complex with Gs protein and Nb35
Map data
Sample
  • Complex: Urocortin1-bound CRF1R in complex Gs and Nb35
    • Protein or peptide: Corticotropin-releasing factor receptor 1
    • Protein or peptide: Urocortin
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Nanobody 35
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID
KeywordsCorticotropin-releasing factor 1 receptor / urocortins1 / Gs protein / GPCR / SIGNALING PROTEIN
Function / homology
Function and homology information


: / corticotropin-releasing hormone binding / histone deacetylase inhibitor activity / regulation of corticosterone secretion / corticotrophin-releasing factor receptor activity / corticotropin-releasing hormone receptor 2 binding / corticotropin secretion / positive regulation of corticotropin secretion / general adaptation syndrome, behavioral process / positive regulation of behavioral fear response ...: / corticotropin-releasing hormone binding / histone deacetylase inhibitor activity / regulation of corticosterone secretion / corticotrophin-releasing factor receptor activity / corticotropin-releasing hormone receptor 2 binding / corticotropin secretion / positive regulation of corticotropin secretion / general adaptation syndrome, behavioral process / positive regulation of behavioral fear response / cellular response to corticotropin-releasing hormone stimulus / parturition / varicosity / negative regulation of voltage-gated calcium channel activity / negative regulation of hormone secretion / positive regulation of cAMP-mediated signaling / behavioral response to ethanol / response to auditory stimulus / drinking behavior / fear response / negative regulation of appetite / corticotropin-releasing hormone receptor 1 binding / neuropeptide hormone activity / positive regulation of vascular permeability / negative regulation of cell size / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / exploration behavior / adrenal gland development / negative regulation of feeding behavior / response to pain / positive regulation of calcium ion import / startle response / associative learning / PKA activation in glucagon signalling / social behavior / hair follicle placode formation / developmental growth / neuropeptide signaling pathway / positive regulation of collagen biosynthetic process / D1 dopamine receptor binding / Synthesis, secretion, and deacylation of Ghrelin / intracellular transport / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / renal water homeostasis / positive regulation of protein localization to cell cortex / Hedgehog 'off' state / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / response to glucocorticoid / cellular response to forskolin / axon terminus / regulation of mitotic spindle organization / regulation of synaptic transmission, glutamatergic / cellular response to glucagon stimulus / positive regulation of cardiac muscle contraction / negative regulation of blood pressure / adenylate cyclase activator activity / regulation of insulin secretion / aerobic respiration / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / trans-Golgi network membrane / positive regulation of DNA replication / positive regulation of translation / Regulation of insulin secretion / female pregnancy / G protein-coupled receptor binding / negative regulation of inflammatory response to antigenic stimulus / sensory perception of sound / bone development / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G protein activity / G-protein activation / platelet aggregation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / response to peptide hormone / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / cognition / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion
Similarity search - Function
GPCR, family 2, corticotropin releasing factor receptor, type 1 / Urocortin/corticotropin-releasing factor / Corticotropin-releasing factor conserved site / Corticotropin-releasing factor family signature. / corticotropin-releasing factor / Corticotropin-releasing factor / GPCR, family 2, corticotropin releasing factor receptor / Corticotropin-releasing factor family / G-protein coupled receptors family 2 signature 1. / : ...GPCR, family 2, corticotropin releasing factor receptor, type 1 / Urocortin/corticotropin-releasing factor / Corticotropin-releasing factor conserved site / Corticotropin-releasing factor family signature. / corticotropin-releasing factor / Corticotropin-releasing factor / GPCR, family 2, corticotropin releasing factor receptor / Corticotropin-releasing factor family / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / G-protein alpha subunit, group S / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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 / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Corticotropin-releasing factor receptor 1 / Urocortin / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMa S / Shen Q
Funding support United States, China, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127710 United States
National Natural Science Foundation of China (NSFC)31770796 China
CitationJournal: Mol Cell / Year: 2020
Title: Molecular Basis for Hormone Recognition and Activation of Corticotropin-Releasing Factor Receptors.
Authors: Shanshan Ma / Qingya Shen / Li-Hua Zhao / Chunyou Mao / X Edward Zhou / Dan-Dan Shen / Parker W de Waal / Peng Bi / Chuntao Li / Yi Jiang / Ming-Wei Wang / Patrick M Sexton / Denise Wootten ...Authors: Shanshan Ma / Qingya Shen / Li-Hua Zhao / Chunyou Mao / X Edward Zhou / Dan-Dan Shen / Parker W de Waal / Peng Bi / Chuntao Li / Yi Jiang / Ming-Wei Wang / Patrick M Sexton / Denise Wootten / Karsten Melcher / Yan Zhang / H Eric Xu /
Abstract: Corticotropin-releasing factor (CRF) and the three related peptides urocortins 1-3 (UCN1-UCN3) are endocrine hormones that control the stress responses by activating CRF1R and CRF2R, two members of ...Corticotropin-releasing factor (CRF) and the three related peptides urocortins 1-3 (UCN1-UCN3) are endocrine hormones that control the stress responses by activating CRF1R and CRF2R, two members of class B G-protein-coupled receptors (GPCRs). Here, we present two cryoelectron microscopy (cryo-EM) structures of UCN1-bound CRF1R and CRF2R with the stimulatory G protein. In both structures, UCN1 adopts a single straight helix with its N terminus dipped into the receptor transmembrane bundle. Although the peptide-binding residues in CRF1R and CRF2R are different from other members of class B GPCRs, the residues involved in receptor activation and G protein coupling are conserved. In addition, both structures reveal bound cholesterol molecules to the receptor transmembrane helices. Our structures define the basis of ligand-binding specificity in the CRF receptor-hormone system, establish a common mechanism of class B GPCR activation and G protein coupling, and provide a paradigm for studying membrane protein-lipid interactions for class B GPCRs.
History
DepositionJun 12, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseFeb 12, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pb0
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20284.png

Downloads & links

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Map

FileDownload / File: emd_20284.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 216 pix.
= 219.024 Å		1.01 Å/pix.
x 216 pix.
= 219.024 Å		1.01 Å/pix.
x 216 pix.
= 219.024 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.1271962 - 0.1910801
Average (Standard dev.)-0.000037213045 (±0.00563427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 219.02402 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z219.024219.024219.024
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.1270.191-0.000

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Supplemental data

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Sample components

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Entire : Urocortin1-bound CRF1R in complex Gs and Nb35

EntireName: Urocortin1-bound CRF1R in complex Gs and Nb35
Components
  • Complex: Urocortin1-bound CRF1R in complex Gs and Nb35
    • Protein or peptide: Corticotropin-releasing factor receptor 1
    • Protein or peptide: Urocortin
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Nanobody 35
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID

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Supramolecule #1: Urocortin1-bound CRF1R in complex Gs and Nb35

SupramoleculeName: Urocortin1-bound CRF1R in complex Gs and Nb35 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Corticotropin-releasing factor receptor 1

MacromoleculeName: Corticotropin-releasing factor receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.509711 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
SequenceString: SLQDQHCESL SLASNISGLQ CNASVDLIGT CWPRSPAGQL VVRPCPAFFY GVRYNTTNNG YRECLANGSW AARVNYSECQ EILNEEKKS KVHYHVAVII NYLGHCISLV ALLVAFVLFL RLRSIRCLRN IIHWNLISAF ILRNATWFVV QLTMSPEVHQ S NVGWCRLV ...String:
SLQDQHCESL SLASNISGLQ CNASVDLIGT CWPRSPAGQL VVRPCPAFFY GVRYNTTNNG YRECLANGSW AARVNYSECQ EILNEEKKS KVHYHVAVII NYLGHCISLV ALLVAFVLFL RLRSIRCLRN IIHWNLISAF ILRNATWFVV QLTMSPEVHQ S NVGWCRLV TAAYNYFHVT NFFWMFGEGC YLHTAIVLTY STDRLRKWMF ICIGWGVPFP IIVAWAIGKL YYDNEKCWFG KR PGVYTDY IYQGPMILVL LINFIFLFNI VRILMTKLRA STTSETIQYR KAVKATLVLL PLLGITYMLF FVNPGEDEVS RVV FIYFNS FLESFQGFFV SVFYCFLNSE VRSAIRKRWH RWQDKHSIRA RVARAMSIP

UniProtKB: Corticotropin-releasing factor receptor 1

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Macromolecule #2: Urocortin

MacromoleculeName: Urocortin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.703277 KDa
Recombinant expressionOrganism: synthetic construct (others)
SequenceString:
DNPSLSIDLT FHLLRTLLEL ARTQSQRERA EQNRIIFDSV

UniProtKB: Urocortin

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Macromolecule #3: Guanine nucleotide-binding protein G(s) subunit alpha isoforms sh...

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.897789 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGYSE EECKQYKAVV YSNTIQSII AIIRAMGRLK IDFGDSARAD DARQLFVLAG AAEEGFMTAE LAGVIKRLWK DSGVQACFNR SREYQLNDSA A YYLNDLDR ...String:
MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGYSE EECKQYKAVV YSNTIQSII AIIRAMGRLK IDFGDSARAD DARQLFVLAG AAEEGFMTAE LAGVIKRLWK DSGVQACFNR SREYQLNDSA A YYLNDLDR IAQPNYIPTQ QDVLRTRVKT TGIFETKFQV DKVNFHMFDV GAQRDERRKW IQCFNDVTAI IFVVASSSYN MV IREDNQT NRLQEALNLF KSIWNNRWLR TISVILFLNK QDLLAEKVLA GKSKIEDYFP EFARYTTPED ATPEPGEDPR VTR AKYFIR DEFLRISTAS GDGRHYCYPH FTCSVDTENI RRVFNDCRDI IQRMHLRQYE LL

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.915496 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSLLQSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String:
MGSLLQSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #6: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.343019 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAQVQLQESG GGLVQPGGSL RLSCAASGFT FSNYKMNWVR QAPGKGLEWV SDISQSGASI SYTGSVKGRF TISRDNAKNT LYLQMNSLK PEDTAVYYCA RCPAPFTRDC FDVTSTTYAY RGQGTQVTVS SHHHHHHEPE A

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Macromolecule #7: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 5 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #8: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 8 / Number of copies: 7 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97386
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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