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- PDB-4k5y: Crystal structure of human corticotropin-releasing factor recepto... -

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Basic information

Entry
Database: PDB / ID: 4k5y
TitleCrystal structure of human corticotropin-releasing factor receptor 1 (CRF1R) in complex with the antagonist CP-376395
ComponentsCorticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct
KeywordsMEMBRANE PROTEIN / RECEPTOR / 7TM / GPCR / FAMILY B / SIGNALLING PROTEIN / G-PROTEIN / MEMBRANE
Function / homology
Function and homology information


regulation of adenylate cyclase activity involved in G protein-coupled receptor signaling pathway / corticotropin-releasing hormone binding / regulation of corticosterone secretion / corticotrophin-releasing factor receptor activity / corticotropin secretion / general adaptation syndrome, behavioral process / cellular response to corticotropin-releasing hormone stimulus / parturition / negative regulation of voltage-gated calcium channel activity / behavioral response to ethanol ...regulation of adenylate cyclase activity involved in G protein-coupled receptor signaling pathway / corticotropin-releasing hormone binding / regulation of corticosterone secretion / corticotrophin-releasing factor receptor activity / corticotropin secretion / general adaptation syndrome, behavioral process / cellular response to corticotropin-releasing hormone stimulus / parturition / negative regulation of voltage-gated calcium channel activity / behavioral response to ethanol / fear response / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / exploration behavior / adrenal gland development / viral release from host cell by cytolysis / activation of adenylate cyclase activity / peptidoglycan catabolic process / female pregnancy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (s) signalling events / host cell cytoplasm / cell surface receptor signaling pathway / endosome / neuron projection / defense response to bacterium / immune response / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, corticotropin releasing factor receptor, type 1 / GPCR, family 2, corticotropin releasing factor receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / 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, corticotropin releasing factor receptor, type 1 / GPCR, family 2, corticotropin releasing factor receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / 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) / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1Q5 / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-PGW / Endolysin / Corticotropin-releasing factor receptor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
ENTEROBACTERIA PHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.977 Å
AuthorsHollenstein, K. / Kean, J. / Bortolato, A. / Cheng, R.K.Y. / Dore, A.S. / Jazayeri, A. / Cooke, R.M. / Weir, M. / Marshall, F.H.
CitationJournal: Nature / Year: 2013
Title: Structure of class B GPCR corticotropin-releasing factor receptor 1.
Authors: Hollenstein, K. / Kean, J. / Bortolato, A. / Cheng, R.K. / Dore, A.S. / Jazayeri, A. / Cooke, R.M. / Weir, M. / Marshall, F.H.
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Corticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct
B: Corticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct
C: Corticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,77219
Polymers151,2893
Non-polymers5,48416
Water1448
1
A: Corticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8486
Polymers50,4301
Non-polymers1,4185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Corticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,88610
Polymers50,4301
Non-polymers3,4579
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Corticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0393
Polymers50,4301
Non-polymers6092
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.559, 123.968, 166.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Corticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct / CRF-R-1 / CRF-R1 / CRFR-1 / Corticotropin-releasing hormone receptor 1 / CRH-R-1 / CRH-R1 / ...CRF-R-1 / CRF-R1 / CRFR-1 / Corticotropin-releasing hormone receptor 1 / CRH-R-1 / CRH-R1 / Endolysin Lysis protein / Muramidase


Mass: 50429.598 Da / Num. of mol.: 3
Fragment: UNP P34998 RESIDUES 104-220, UNP P00720 RESIDUES 2-161, UNP P34998 RESIDUES 224-373
Mutation: v120a, l144a, w156a, s160a, n40s, a41v, c54s, c97s, t151a, k228a, f260a, i277a, y309a, f330a, s349a, y363a
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human), (gene. exp.) ENTEROBACTERIA PHAGE T4 (virus)
Gene: CRF1R, CRFR, CRFR1, CRHR, CRHR1, E / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P34998, UniProt: P00720

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Non-polymers , 7 types, 24 molecules

#2: Chemical ChemComp-1Q5 / 3,6-dimethyl-N-(pentan-3-yl)-2-(2,4,6-trimethylphenoxy)pyridin-4-amine


Mass: 326.476 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N2O
#3: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CRYSTALLIZED SEQUENCE REFERS TO ISOFORM 2 CRF-R2 OF CORTICOTROPIN-RELEASING FACTOR RECEPTOR 1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 35

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 295.6 K / Method: lipidic cubic phase / pH: 5.5
Details: 30% (v/v) PEG 400, 0.2M lithium sulphate, 0.1M sodium citrate 5.5, Lipidic Cubic Phase, temperature 295.6K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2012
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.97→34.14 Å / Num. all: 32141 / Num. obs: 30535 / % possible obs: 86.3 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 6.7
Reflection shellResolution: 2.97→3.14 Å / Redundancy: 2 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.9 / % possible all: 68.2

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3EML; 3PBL

3eml

3pbl


Resolution: 2.977→34.14 Å / SU ML: 0.45 / Isotropic thermal model: ISOTROPIC / σ(F): 1.93 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 1586 4.94 %
Rwork0.2417 --
obs0.2428 30535 85.67 %
all-81748 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.977→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8477 0 338 8 8823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129023
X-RAY DIFFRACTIONf_angle_d1.39512180
X-RAY DIFFRACTIONf_dihedral_angle_d13.7323287
X-RAY DIFFRACTIONf_chiral_restr0.1091349
X-RAY DIFFRACTIONf_plane_restr0.0111457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9774-3.07340.36381080.34211964X-RAY DIFFRACTION62
3.0734-3.18320.37891410.3222567X-RAY DIFFRACTION81
3.1832-3.31050.32731300.29552619X-RAY DIFFRACTION82
3.3105-3.4610.29471410.272733X-RAY DIFFRACTION85
3.461-3.64330.28091160.25292743X-RAY DIFFRACTION85
3.6433-3.87130.26391580.23292886X-RAY DIFFRACTION90
3.8713-4.16970.26131590.2232898X-RAY DIFFRACTION90
4.1697-4.58840.25291470.21422973X-RAY DIFFRACTION92
4.5884-5.25030.22051590.20983007X-RAY DIFFRACTION93
5.2503-6.6070.2831580.24573012X-RAY DIFFRACTION91
6.607-34.15720.21451690.2273124X-RAY DIFFRACTION91

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