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- EMDB-20277: CRF1 Receptor Gs GPCR protein complex with CRF1 peptide. -

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Basic information

Entry
Database: EMDB / ID: EMD-20277
TitleCRF1 Receptor Gs GPCR protein complex with CRF1 peptide.
Map dataPost-processed map
Sample
  • Complex: Complex of active-state Corticotropin-releasing hormone receptor 1 with heterotrimeric Gs protein.
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Corticotropin-releasing factor receptor 1
      • Protein or peptide: 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: Corticotropin-releasing factor receptor 1
    • Complex: Nanobody 35
      • Protein or peptide: Nanobody 35
    • Complex: Corticoliberin
      • Protein or peptide: Corticoliberin
  • Ligand: water
KeywordsGPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


corticotropin-releasing hormone activity / positive regulation of digestive system process / positive regulation of corticosterone secretion / corticotropin-releasing hormone binding / positive regulation of circadian sleep/wake cycle, wakefulness / negative regulation of circadian sleep/wake cycle, REM sleep / corticotropin-releasing hormone receptor activity / regulation of corticosterone secretion / corticotrophin-releasing factor receptor activity / corticotropin-releasing hormone receptor 2 binding ...corticotropin-releasing hormone activity / positive regulation of digestive system process / positive regulation of corticosterone secretion / corticotropin-releasing hormone binding / positive regulation of circadian sleep/wake cycle, wakefulness / negative regulation of circadian sleep/wake cycle, REM sleep / corticotropin-releasing hormone receptor activity / regulation of corticosterone secretion / corticotrophin-releasing factor receptor activity / corticotropin-releasing hormone receptor 2 binding / corticotropin secretion / positive regulation of corticotropin secretion / neuronal dense core vesicle lumen / positive regulation of cortisol secretion / regulation of serotonin secretion / negative regulation of glucagon secretion / glucocorticoid biosynthetic process / general adaptation syndrome, behavioral process / positive regulation of behavioral fear response / cellular response to corticotropin-releasing hormone stimulus / MECP2 regulates transcription of neuronal ligands / negative regulation of luteinizing hormone secretion / varicosity / negative regulation of norepinephrine secretion / parturition / hormone-mediated apoptotic signaling pathway / negative regulation of voltage-gated calcium channel activity / monoatomic ion homeostasis / negative regulation of epinephrine secretion / positive regulation of cAMP-mediated signaling / behavioral response to ethanol / response to ether / corticotropin-releasing hormone receptor 1 binding / neuropeptide hormone activity / fear response / synaptic transmission, dopaminergic / negative regulation of systemic arterial blood pressure / regulation of NMDA receptor activity / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / cellular response to cocaine / diterpenoid metabolic process / exploration behavior / adrenal gland development / response to corticosterone / response to pain / response to aldosterone / hypothalamus development / positive regulation of calcium ion import / locomotory exploration behavior / associative learning / PKA activation in glucagon signalling / positive regulation of insulin secretion involved in cellular response to glucose stimulus / hair follicle placode formation / response to immobilization stress / developmental growth / D1 dopamine receptor binding / intracellular transport / renal water homeostasis / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / cellular response to glucagon stimulus / adenylate cyclase activator activity / regulation of insulin secretion / cellular response to dexamethasone stimulus / trans-Golgi network membrane / female pregnancy / long-term synaptic potentiation / negative regulation of inflammatory response to antigenic stimulus / lung development / G protein-coupled receptor activity / bone development / postsynaptic density membrane / hormone activity / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / platelet aggregation / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cognition / 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 activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / response to estrogen / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins
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 / 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
Corticoliberin / Corticotropin-releasing factor receptor 1 / 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
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsBelousoff MJ / Liang YL
Funding support Australia, Japan, 5 items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia)1120919 Australia
National Health and Medical Research Council (Australia)1159006 Australia
National Health and Medical Research Council (Australia)1150083 Australia
Japan Society for the Promotion of ScienceKAKENHI #18H06043 Japan
Japan Science and TechnologyPRESTO #18069571 Japan
CitationJournal: Mol Cell / Year: 2020
Title: Toward a Structural Understanding of Class B GPCR Peptide Binding and Activation.
Authors: Yi-Lynn Liang / Matthew J Belousoff / Peishen Zhao / Cassandra Koole / Madeleine M Fletcher / Tin T Truong / Villy Julita / George Christopoulos / H Eric Xu / Yan Zhang / Maryam Khoshouei / ...Authors: Yi-Lynn Liang / Matthew J Belousoff / Peishen Zhao / Cassandra Koole / Madeleine M Fletcher / Tin T Truong / Villy Julita / George Christopoulos / H Eric Xu / Yan Zhang / Maryam Khoshouei / Arthur Christopoulos / Radostin Danev / Patrick M Sexton / Denise Wootten /
Abstract: Class B G protein-coupled receptors (GPCRs) are important therapeutic targets for major diseases. Here, we present structures of peptide and Gs-bound pituitary adenylate cyclase-activating peptide, ...Class B G protein-coupled receptors (GPCRs) are important therapeutic targets for major diseases. Here, we present structures of peptide and Gs-bound pituitary adenylate cyclase-activating peptide, PAC1 receptor, and corticotropin-releasing factor (CRF), (CRF1) receptor. Together with recently solved structures, these provide coverage of the major class B GPCR subfamilies. Diverse orientations of the extracellular domain to the receptor core in different receptors are at least partially dependent on evolutionary conservation in the structure and nature of peptide interactions. Differences in peptide interactions to the receptor core also influence the interlinked TM2-TM1-TM6/ECL3/TM7 domain, and this is likely important in their diverse signaling. However, common conformational reorganization of ECL2, linked to reorganization of ICL2, modulates G protein contacts. Comparison between receptors reveals ICL2 as a key domain forming dynamic G protein interactions in a receptor- and ligand-specific manner. This work advances our understanding of class B GPCR activation and Gs coupling.
History
DepositionJun 10, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseFeb 5, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-6p9x
  • Surface level: 0.04
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20277.png

Downloads & links

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Map

FileDownload / File: emd_20277.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 176 pix.
= 212.48 Å		1.21 Å/pix.
x 176 pix.
= 212.48 Å		1.21 Å/pix.
x 176 pix.
= 212.48 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.20727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.04
Minimum - Maximum-0.2589433 - 0.44343185
Average (Standard dev.)0.000010454083 (±0.012369758)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 212.48004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.20727272727271.20727272727271.2072727272727
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z212.480212.480212.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS176176176
D min/max/mean-0.2590.4430.000

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Supplemental data

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Mask #1

Fileemd_20277_msk_1.map
Projections & Slices
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Additional map: additional map

Fileemd_20277_additional.map
Annotationadditional map
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Histogram

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Half map: half map - even

Fileemd_20277_half_map_1.map
Annotationhalf map - even
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map - odd

Fileemd_20277_half_map_2.map
Annotationhalf map - odd
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Sample components

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Entire : Complex of active-state Corticotropin-releasing hormone receptor ...

EntireName: Complex of active-state Corticotropin-releasing hormone receptor 1 with heterotrimeric Gs protein.
Components
  • Complex: Complex of active-state Corticotropin-releasing hormone receptor 1 with heterotrimeric Gs protein.
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Corticotropin-releasing factor receptor 1
      • Protein or peptide: 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: Corticotropin-releasing factor receptor 1
    • Complex: Nanobody 35
      • Protein or peptide: Nanobody 35
    • Complex: Corticoliberin
      • Protein or peptide: Corticoliberin
  • Ligand: water

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Supramolecule #1: Complex of active-state Corticotropin-releasing hormone receptor ...

SupramoleculeName: Complex of active-state Corticotropin-releasing hormone receptor 1 with heterotrimeric Gs protein.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: Guanine nucleotide-binding protein G(s) subunit alpha isoforms sh...

SupramoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit ...Name: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Corticotropin-releasing factor receptor 1
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Nanobody 35

SupramoleculeName: Nanobody 35 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lama glama (llama)

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Supramolecule #4: Corticoliberin

SupramoleculeName: Corticoliberin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.700418 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE ...String:
MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE YQLIDCAQYF LDKIDVIKQA DYVPSDQDLL RCRVLTSGIF ETKFQVDKVN FHMFDVGGQR DERRKWIQCF ND VTAIIFV VASSSYNMVI REDNQTNRLQ EALKLFDSIW NNKWLRDTSV ILFLNKQDLL AEKVLAGKSK IEDYFPEFAR YTT PEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCA VDTENIRRVF NDCRDIIQRM HLRQYELL

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

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Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.534062 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHGSS GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC R FLDDNQIV ...String:
MHHHHHHGSS GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC R FLDDNQIV TSSGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD IN AICFFPN GNAFATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAG HDNRVS CLGVTDDGMA VATGSWDSFL KIWN

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

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #4: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.140742 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSSH HHHHHEPEA

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Macromolecule #5: Corticotropin-releasing factor receptor 1

MacromoleculeName: Corticotropin-releasing factor receptor 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.392109 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DYKDDDDLEV LFQGPASLQD QHCESLSLAS NISGLQCNAS VDLIGTCWPR SPAGQLVVRP CPAFFYGVRY NTTNNGYREC LANGSWAAR VNYSECQEIL NEEKKSKVHY HVAVIINYLG HCISLVALLV AFVLFLRLRS IRCLRNIIHW NLISAFILRN A TWFVVQLT ...String:
DYKDDDDLEV LFQGPASLQD QHCESLSLAS NISGLQCNAS VDLIGTCWPR SPAGQLVVRP CPAFFYGVRY NTTNNGYREC LANGSWAAR VNYSECQEIL NEEKKSKVHY HVAVIINYLG HCISLVALLV AFVLFLRLRS IRCLRNIIHW NLISAFILRN A TWFVVQLT MSPEVHQSNV GWCRLVTAAY NYFHVTNFFW MFGEGCYLHT AIVLTYTTDR LRKWMFICIG WGVPFPIIVA WA IGKLYYD NEKCWFGKRP GVYTDYIYQG PMILVLLINF IFLFNIVRIL MTKLRASTTS ETIQYRKAVK ATLVLLPLLG ITY MLFFVN PGEDEVSRVV FIYFNSFLES FQGFFVSVFY CFLNSEVRSA IRKRWHRWQD KHSIRARVAR AMSIPTSPTR VSFH SIKQS TAVPAGLEVL FQGPHHHHHH HH

UniProtKB: Corticotropin-releasing factor receptor 1

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Macromolecule #6: Corticoliberin

MacromoleculeName: Corticoliberin / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.764481 KDa
SequenceString:
SEEPPISLDL TFHLLREVLE MARAEQLAQQ AHSNRKLMEI I

UniProtKB: Corticoliberin

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 17 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 3.7 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 516000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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