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- PDB-3ehs: Crystal structure of the extracellular domain of human corticotro... -

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Basic information

Entry
Database: PDB / ID: 3ehs
TitleCrystal structure of the extracellular domain of human corticotropin releasing factor receptor type 1 (CRFR1)
Componentsfusion protein of CRFR1 extracellular domain and MBP
KeywordsMEMBRANE PROTEIN / G protein-coupled receptor / corticotropin releasing factor / SCR fold / MBP fusion / extracellular domain / Sugar transport / Transport / Cell membrane / Glycoprotein / Membrane / Phosphoprotein / Receptor / Transducer / Transmembrane
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-releasing hormone receptor activity / corticotropin secretion / general adaptation syndrome, behavioral process / parturition / cellular response to corticotropin-releasing hormone stimulus / negative regulation of voltage-gated calcium channel activity ...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-releasing hormone receptor activity / corticotropin secretion / general adaptation syndrome, behavioral process / parturition / cellular response to corticotropin-releasing hormone stimulus / 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 / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / activation of adenylate cyclase activity / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / female pregnancy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / outer membrane-bounded periplasmic space / G alpha (s) signalling events / periplasmic space / cell surface receptor signaling pathway / endosome / neuron projection / immune response / DNA damage response / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, corticotropin releasing factor receptor, type 1 / GPCR, family 2, corticotropin releasing factor receptor / 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 ...GPCR, family 2, corticotropin releasing factor receptor, type 1 / GPCR, family 2, corticotropin releasing factor receptor / 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 / 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 / molecular replacement / Resolution: 2.76 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 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 26, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _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 / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _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.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8892
Polymers52,5471
Non-polymers3421
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.018, 112.018, 145.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-132-

HOH

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Components

#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: 52547.145 Da / Num. of mol.: 1
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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.35 Å3/Da / Density % sol: 71.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.7
Details: NaCl, sucrose, sodium acetate, pH 4.7, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / 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: 2.75→50 Å / Num. obs: 24253 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 33.26
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.99 / % possible all: 90.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3c4m


Resolution: 2.76→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 23.417 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1238 5.1 %RANDOM
Rwork0.207 ---
obs0.209 22955 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.97 Å2 / Biso mean: 93.281 Å2 / Biso min: 64.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2---1.36 Å20 Å2
3---2.71 Å2
Refinement stepCycle: LAST / Resolution: 2.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 23 6 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223652
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.9644966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08825.671164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63615593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3921510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022788
X-RAY DIFFRACTIONr_nbd_refined0.2050.21608
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.26
X-RAY DIFFRACTIONr_mcbond_it0.461.52329
X-RAY DIFFRACTIONr_mcangle_it0.7823641
X-RAY DIFFRACTIONr_scbond_it1.17131529
X-RAY DIFFRACTIONr_scangle_it1.8344.51325
LS refinement shellResolution: 2.76→2.828 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 76 -
Rwork0.312 1457 -
all-1533 -
obs--86.66 %
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)
14-1.4976-1.66016.94232.78967.28340.21810.2472-0.04230.0298-0.3581.1173-0.0476-0.58880.1399-0.25750.020.0031-0.394-0.1928-0.082418.62360.931415.7966
27.7666-0.7552-3.32957.8821-2.08277.1507-0.2447-0.4019-0.43720.3430.3095-0.22360.1470.3746-0.0648-0.44440.06820.0805-0.3790.0065-0.388443.540930.66580.6971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-348 - 23
2X-RAY DIFFRACTION1A126
3X-RAY DIFFRACTION2A24 - 108

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