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- PDB-4z9g: Crystal structure of human corticotropin-releasing factor recepto... -

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Basic information

Entry
Database: PDB / ID: 4z9g
TitleCrystal structure of human corticotropin-releasing factor receptor 1 (CRF1R) in complex with the antagonist CP-376395 in a hexagonal setting with translational non-crystallographic symmetry
ComponentsCorticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
KeywordsSIGNALING PROTEIN / 7TM / GPCR / FAMILY B / G-PROTEIN / MEMBRANE / MEMBRANE PROTEIN / RECEPTOR / tNCS / HEXAGONAL
Function / homology
Function and homology information


corticotropin-releasing hormone binding / corticotropin-releasing hormone receptor activity / 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 ...corticotropin-releasing hormone binding / corticotropin-releasing hormone receptor activity / 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 / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / adrenal gland development / exploration behavior / viral release from host cell by cytolysis / activation of adenylate cyclase activity / peptidoglycan catabolic process / female pregnancy / G protein-coupled receptor activity / postsynaptic density membrane / 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 / neuron projection / endosome / defense response to bacterium / immune response / glutamatergic synapse / 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. / : / 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, corticotropin releasing factor receptor, type 1 / GPCR, family 2, corticotropin releasing factor receptor / 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. / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-1Q5 / OLEIC ACID / Endolysin / Corticotropin-releasing factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage RB51 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.183 Å
AuthorsDore, A.S. / Bortolato, A. / Hollenstein, K. / Cheng, R.K.Y. / Read, R.J. / Marshall, F.H.
CitationJournal: Curr Mol Pharmacol / Year: 2017
Title: Decoding Corticotropin-Releasing Factor Receptor Type 1 Crystal Structures.
Authors: Dore, A.S. / Bortolato, A. / Hollenstein, K. / Cheng, R.K.Y. / Read, R.J. / Marshall, F.H.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)156,02419
Polymers151,9323
Non-polymers4,09216
Water00
1
A: Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0107
Polymers50,6441
Non-polymers1,3666
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8185
Polymers50,6441
Non-polymers1,1744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1967
Polymers50,6441
Non-polymers1,5526
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.359, 189.359, 88.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1 / CRFR-1 / Corticotropin-releasing hormone receptor 1


Mass: 50643.855 Da / Num. of mol.: 3
Mutation: V120A, L144A, W156A, S160A, N1040S, A1041V, C1054S, C1097S, T1151A, S222L, K228A, F260A, I277A, Y309A, F330A, S349A, Y363A,V120A, L144A, W156A, S160A, N1040S, A1041V, C1054S, C1097S, ...Mutation: V120A, L144A, W156A, S160A, N1040S, A1041V, C1054S, C1097S, T1151A, S222L, K228A, F260A, I277A, Y309A, F330A, S349A, Y363A,V120A, L144A, W156A, S160A, N1040S, A1041V, C1054S, C1097S, T1151A, S222L, K228A, F260A, I277A, Y309A, F330A, S349A, Y363A,V120A, L144A, W156A, S160A, N1040S, A1041V, C1054S, C1097S, T1151A, S222L, K228A, F260A, I277A, Y309A, F330A, S349A, Y363A
Source method: isolated from a genetically manipulated source
Details: CORTICOTROPIN-RELEASING FACTOR RECEPTOR 1, T4-LYSOZYME CHIMERIC CONSTRUCT
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB51 (virus)
Gene: CRHR1, CRFR, CRFR1, CRHR, e, RB51ORF131 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P34998, UniProt: C3V2B5, lysozyme
#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C18H34O2
#3: 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.37 % / Description: hexagonal prisms
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
PH range: 5.3 - 5.7 / Temp details: None

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Data collection

DiffractionMean temperature: 200 K / Ambient temp details: None
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2012
RadiationMonochromator: Graphite Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.12
ReflectionResolution: 3.18→45.48 Å / Num. obs: 28527 / % possible obs: 93.7 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.094 / Net I/σ(I): 6.4 / Num. measured all: 109312 / Scaling rejects: 49
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.18-3.382.50.721.81028340330.0890.48182
9.55-45.484.90.06822.5557911390.9950.03296.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASERphasing
PHENIX1.8.1refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K5Y

4k5y


Resolution: 3.183→19.91 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.78 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2886 1528 5.38 %Random Selection
Rwork0.2444 26923 --
obs0.2467 28393 93.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.91 Å2 / Biso mean: 90.6062 Å2 / Biso min: 19.8 Å2
Refinement stepCycle: final / Resolution: 3.183→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9980 0 264 0 10244
Biso mean--85.53 --
Num. residues----1239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610476
X-RAY DIFFRACTIONf_angle_d0.88214150
X-RAY DIFFRACTIONf_chiral_restr0.0581579
X-RAY DIFFRACTIONf_plane_restr0.0041725
X-RAY DIFFRACTIONf_dihedral_angle_d15.1663802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1855-3.29890.411250.34542245237075
3.2989-3.43030.36571500.32352574272485
3.4303-3.58550.32491280.30392644277288
3.5855-3.77320.34151440.28352688283289
3.7732-4.00770.31361500.2522760291091
4.0077-4.3140.26281320.23792749288191
4.314-4.74250.22361560.2222778293491
4.7425-5.41590.28761460.22532793293992
5.4159-6.77550.34151770.26422814299192
6.7755-19.50210.21981490.18582878302792
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.09450.0311-0.05810.0154-0.0241-0.02030.0731-0.52040.0064-0.04580.20610.0581-0.01050.1789-00.39460.02250.07890.0013-0.03690.40643.179427.4007-16.6845
2-0.02280.0534-0.07430.01530.00240.03090.18820.15580.01030.1009-0.1175-0.03920.037-0.1268-00.6331-0.0711-0.04550.56230.07080.529416.65936.883-60.8924
30.04570.04690.0060.0334-0.0437-0.0020.17250.02450.24620.05730.1296-0.1576-0.0172-0.112400.4479-0.0122-0.02250.3913-0.01260.357912.809337.1125-24.201
40.09560.00710.01420.028-0.0130.00190.12280.00130.0761-0.07780.15220.0379-0.037-0.1774-00.48540.06210.00670.3901-0.02620.415-4.481938.3129-23.1868
50.0527-0.05070.04220.0695-0.0517-0.00670.11360.03890.066-0.06110.28810.04340.0915-0.0149-00.4926-0.0088-0.09390.35690.03040.3816-7.930485.3426-32.8259
60.21820.0356-0.0597-0.0055-0.14730.0643-0.0263-0.06450.0392-0.05530.00660.104-0.0184-0.0264-00.54870.114-0.08510.4367-0.07190.4557.297772.1673.2134
70.02350.03380.01280.03250.04490.00120.29110.1613-0.2183-0.17160.1489-0.0189-0.0647-0.2188-00.6294-0.0614-0.17950.3251-0.1090.5045-0.050167.2093-31.9623
80.0331-0.0009-0.0090.0215-0.01760.0005-0.10720.0728-0.12860.04640.02680.0573-0.0068-0.039200.5703-0.027-0.17250.3995-0.0230.6136-15.628274.7186-21.8025
90.0073-0.0257-0.00570.014-0.02830.02150.23810.0758-0.14110.10960.14390.32310.0292-0.27170-0.49490.3309-0.55850.0480.36310.0687-25.8254100.8025-31.013
10-0.03020.0144-0.01250.02110.01840.01510.26850.1651-0.00730.03980.2519-0.0418-0.01460.077300.4555-0.7807-0.00880.56880.65730.7823-34.706772.93458.6884
110.11610.0672-0.08020.14860.01430.04210.1031-0.0637-0.0697-0.04440.07680.1724-0.12240.0725-00.4751-0.0745-0.11930.52470.09340.4858-28.096189.6924-4.9501
120.05250.0235-0.02410.0421-0.02190.00610.0162-0.0517-0.0397-0.0878-0.11220.14560.019-0.0365-00.2639-0.1004-0.05710.68420.10860.444-37.1369106.1556-24.3918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 111 through 217 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 1155 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1156 through 303 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 304 through 372 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 113 through 185 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 186 through 237 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 238 through 296 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 297 through 372 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 112 through 217 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 218 through 1080 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 1081 through 303 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 304 through 370 )C0

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