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Basic information

Entry
Database: PDB / ID: 3ehu
TitleCrystal structure of the extracellular domain of human corticotropin releasing factor receptor type 1 (CRFR1) in complex with CRF
Components
  • Corticoliberin
  • FUSION PROTEIN OF CRFR1 EXTRACELLULAR DOMAIN AND MBP
KeywordsMEMBRANE PROTEIN / G protein-coupled receptor / corticotropin releasing factor / CRF / SCR fold / MBP fusion / extracellular domain / Sugar transport / Transport / Cell membrane / Glycoprotein / Membrane / Phosphoprotein / Receptor / Transducer / Transmembrane / Amidation / Cleavage on pair of basic residues / Hormone / Secreted
Function / homology
Function and homology information


corticotropin-releasing hormone activity / positive regulation of digestive system process / positive regulation of corticosterone secretion / regulation of adenylate cyclase activity involved in G protein-coupled receptor signaling pathway / corticotropin-releasing hormone binding / positive regulation of circadian sleep/wake cycle, wakefulness / negative regulation of circadian sleep/wake cycle, REM sleep / regulation of corticosterone secretion / corticotrophin-releasing factor receptor activity / corticotropin-releasing hormone receptor activity ...corticotropin-releasing hormone activity / positive regulation of digestive system process / positive regulation of corticosterone secretion / regulation of adenylate cyclase activity involved in G protein-coupled receptor signaling pathway / corticotropin-releasing hormone binding / positive regulation of circadian sleep/wake cycle, wakefulness / negative regulation of circadian sleep/wake cycle, REM sleep / regulation of corticosterone secretion / corticotrophin-releasing factor receptor activity / corticotropin-releasing hormone receptor activity / corticotropin-releasing hormone receptor 2 binding / corticotropin secretion / positive regulation of corticotropin secretion / positive regulation of cortisol secretion / regulation of serotonin secretion / general adaptation syndrome, behavioral process / negative regulation of glucagon secretion / MECP2 regulates transcription of neuronal ligands / positive regulation of behavioral fear response / glucocorticoid biosynthetic process / negative regulation of norepinephrine secretion / parturition / hormone-mediated apoptotic signaling pathway / monoatomic ion homeostasis / negative regulation of luteinizing hormone secretion / negative regulation of epinephrine secretion / cellular response to corticotropin-releasing hormone stimulus / negative regulation of voltage-gated calcium channel activity / varicosity / behavioral response to ethanol / positive regulation of cAMP-mediated signaling / response to ether / fear response / neuropeptide hormone activity / synaptic transmission, dopaminergic / G protein-coupled peptide receptor activity / negative regulation of systemic arterial blood pressure / Class B/2 (Secretin family receptors) / regulation of NMDA receptor activity / cellular response to cocaine / diterpenoid metabolic process / exploration behavior / response to aldosterone / adrenal gland development / hypothalamus development / response to pain / response to corticosterone / detection of maltose stimulus / maltose transport complex / positive regulation of calcium ion import / locomotory exploration behavior / carbohydrate transport / positive regulation of insulin secretion involved in cellular response to glucose stimulus / associative learning / carbohydrate transmembrane transporter activity / maltose binding / response to immobilization stress / maltose transport / maltodextrin transmembrane transport / corticotropin-releasing hormone receptor 1 binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / activation of adenylate cyclase activity / ATP-binding cassette (ABC) transporter complex / cellular response to dexamethasone stimulus / cell chemotaxis / female pregnancy / long-term synaptic potentiation / lung development / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / response to estrogen / outer membrane-bounded periplasmic space / G alpha (s) signalling events / chemical synaptic transmission / perikaryon / neuron apoptotic process / response to ethanol / periplasmic space / learning or memory / cell surface receptor signaling pathway / endosome / response to xenobiotic stimulus / inflammatory response / neuron projection / positive regulation of protein phosphorylation / immune response / negative regulation of gene expression / signaling receptor binding / synapse / DNA damage response / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / membrane / plasma membrane
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 / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold ...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 / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / 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) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / DI(HYDROXYETHYL)ETHER / Corticoliberin / Maltose/maltodextrin-binding periplasmic protein / Corticotropin-releasing factor receptor 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsPioszak, A.A. / Xu, H.E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Molecular Recognition of Corticotropin-releasing Factor by Its G-protein-coupled Receptor CRFR1.
Authors: Pioszak, A.A. / Parker, N.R. / Suino-Powell, K. / Xu, H.E.
History
DepositionSep 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / reflns ...entity_src_gen / reflns / reflns_shell / struct_conn / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _reflns.pdbx_Rmerge_I_obs ..._entity_src_gen.gene_src_common_name / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUSION PROTEIN OF CRFR1 EXTRACELLULAR DOMAIN AND MBP
B: FUSION PROTEIN OF CRFR1 EXTRACELLULAR DOMAIN AND MBP
C: Corticoliberin
D: Corticoliberin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,22512
Polymers109,8304
Non-polymers1,3958
Water8,107450
1
A: FUSION PROTEIN OF CRFR1 EXTRACELLULAR DOMAIN AND MBP
C: Corticoliberin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6136
Polymers54,9152
Non-polymers6984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-6 kcal/mol
Surface area21700 Å2
MethodPISA
2
B: FUSION PROTEIN OF CRFR1 EXTRACELLULAR DOMAIN AND MBP
D: Corticoliberin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6136
Polymers54,9152
Non-polymers6984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-7 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.203, 63.480, 85.875
Angle α, β, γ (deg.)99.750, 106.280, 101.670
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABCD

#1: Protein FUSION PROTEIN OF CRFR1 EXTRACELLULAR DOMAIN AND MBP / MMBP / Maltodextrin-binding protein / CRF-R / CRF1 / Corticotropin-releasing hormone receptor 1 / CRH-R 1


Mass: 52605.180 Da / Num. of mol.: 2 / Mutation: A(-25)E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P34998
#2: Protein/peptide Corticoliberin / Corticotropin-releasing hormone / Corticotropin-releasing factor / CRF


Mass: 2309.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: P06850
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 456 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.75
Details: PEG MME 550, calcium chloride, tert-butanol, Bis-Tris, pH 6.75, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 64919 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.49
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.32 / % possible all: 75.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 3C4M, 3EHS

3c4m

3ehs


Resolution: 1.96→39.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.703 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3254 5 %RANDOM
Rwork0.209 ---
obs0.212 61357 94.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 64.53 Å2 / Biso mean: 30.115 Å2 / Biso min: 10.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20.9 Å20.38 Å2
2--1.73 Å2-0.24 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.96→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7044 0 90 450 7584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227300
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9699910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48825.625320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.316151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5721520
X-RAY DIFFRACTIONr_chiral_restr0.0830.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025526
X-RAY DIFFRACTIONr_nbd_refined0.2040.23393
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2495
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.220
X-RAY DIFFRACTIONr_mcbond_it0.6531.54698
X-RAY DIFFRACTIONr_mcangle_it1.02927270
X-RAY DIFFRACTIONr_scbond_it1.71333041
X-RAY DIFFRACTIONr_scangle_it2.6494.52640
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 161 -
Rwork0.249 3543 -
all-3704 -
obs--74.08 %
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)
11.93330.97640.74381.53230.61811.1799-0.01380.0616-0.083-0.08730.0295-0.00260.09780.0321-0.0157-0.13450.03560.0183-0.1625-0.0042-0.1443-33.4016-48.136114.113
21.8636-0.6216-0.66291.25950.5411.30550.0301-0.0970.11280.1019-0.04890.0146-0.0721-0.01050.0187-0.1389-0.0157-0.0093-0.1591-0.0192-0.1423-33.9795-1.564265.1045
37.48261.9124-0.10347.9862-2.65996.3839-0.17350.7601-0.4355-1.02240.24510.10750.9079-0.2528-0.07160.1572-0.0507-0.03690.02660.0543-0.0862-39.2696-23.178579.1189
47.5378-0.6142-0.36816.2891-2.93765.8886-0.0993-0.560.45620.95440.20110.2082-0.8027-0.2595-0.10180.14510.01180.03770.01850.0873-0.072-39.0952-26.7625100.1341
578.249717.490928.46458.43346.388718.13120.30010.41190.0198-0.5507-0.33510.6422-0.1727-0.20340.0350.1932-0.0248-0.00280.13440.07990.1214-57.915-22.24482.707
681.9912-14.5127-32.45918.90394.962617.6355-0.41240.4642-0.67430.453-0.21320.7990.4661-0.4540.62560.1674-0.0078-0.00710.15610.07390.1178-57.6606-27.725196.3277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-348 - 23
2X-RAY DIFFRACTION1A503
3X-RAY DIFFRACTION2B-348 - 23
4X-RAY DIFFRACTION2B503
5X-RAY DIFFRACTION3A27 - 104
6X-RAY DIFFRACTION4B27 - 104
7X-RAY DIFFRACTION5C26 - 42
8X-RAY DIFFRACTION6D26 - 42

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