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

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Basic information

Entry
Database: PDB / ID: 3eht
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 / 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 / diterpenoid metabolic process / 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 / diterpenoid metabolic process / 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 corticosterone secretion / positive regulation of cortisol secretion / positive regulation of corticotropin secretion / negative regulation of glucagon secretion / positive regulation of behavioral fear response / general adaptation syndrome, behavioral process / cellular response to corticotropin-releasing hormone stimulus / glucocorticoid biosynthetic process / negative regulation of luteinizing hormone secretion / varicosity / MECP2 regulates transcription of neuronal ligands / parturition / monoatomic ion homeostasis / regulation of serotonin secretion / hormone-mediated apoptotic signaling pathway / negative regulation of norepinephrine secretion / negative regulation of voltage-gated calcium channel activity / neuronal dense core vesicle lumen / negative regulation of epinephrine secretion / response to ether / behavioral response to ethanol / neuropeptide hormone activity / corticotropin-releasing hormone receptor 1 binding / fear response / synaptic transmission, dopaminergic / response to aldosterone / negative regulation of systemic arterial blood pressure / regulation of NMDA receptor activity / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / cellular response to cocaine / adrenal gland development / response to pain / response to corticosterone / detection of maltose stimulus / positive regulation of calcium ion import / hypothalamus development / maltose transport complex / exploration behavior / response to immobilization stress / carbohydrate transport / positive regulation of cAMP/PKA signal transduction / locomotory exploration behavior / associative learning / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / cellular response to dexamethasone stimulus / positive regulation of insulin secretion involved in cellular response to glucose stimulus / activation of adenylate cyclase activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / lung development / cell chemotaxis / female pregnancy / G protein-coupled receptor activity / hormone activity / postsynaptic density membrane / response to estrogen / long-term synaptic potentiation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / outer membrane-bounded periplasmic space / neuron apoptotic process / response to ethanol / perikaryon / G alpha (s) signalling events / chemical synaptic transmission / learning or memory / periplasmic space / cell surface receptor signaling pathway / endosome / neuron projection / immune response / response to xenobiotic stimulus / inflammatory response / signaling receptor binding / negative regulation of gene expression / positive regulation of cell population proliferation / synapse / DNA damage response / positive regulation of gene expression / glutamatergic synapse / 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. / : / 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. / 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 / Corticoliberin / Maltose/maltodextrin-binding periplasmic protein / Corticotropin-releasing factor receptor 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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 1.2Feb 8, 2017Group: Structure summary
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: reflns / reflns_shell ...reflns / reflns_shell / struct_conn / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs ..._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 / 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_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 2.1Oct 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
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Corticoliberin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6243
Polymers54,2822
Non-polymers3421
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.977, 112.977, 158.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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: 52529.082 Da / Num. of mol.: 1 / Mutation: F(-257)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: 1753.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / 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.: 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
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: 4.65 Å3/Da / Density % sol: 73.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.25
Details: PEG 3350, Lithium sulfate, Bis-Tris, pH 6.25, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99999 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 14697 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 20.81
Reflection shellResolution: 3.4→3.52 Å / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 1.88 / % possible all: 97.2

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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: 3.4→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 51.335 / SU ML: 0.367 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.252 739 5 %RANDOM
Rwork0.218 ---
obs0.22 13897 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.27 Å2 / Biso mean: 155.517 Å2 / Biso min: 137.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 23 0 3609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223698
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.9635025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3885461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30525.576165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19715606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.461511
X-RAY DIFFRACTIONr_chiral_restr0.0670.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022816
X-RAY DIFFRACTIONr_nbd_refined0.1920.21658
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.25
X-RAY DIFFRACTIONr_mcbond_it0.321.52348
X-RAY DIFFRACTIONr_mcangle_it0.59223688
X-RAY DIFFRACTIONr_scbond_it0.65331538
X-RAY DIFFRACTIONr_scangle_it1.1894.51337
LS refinement shellResolution: 3.4→3.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 60 -
Rwork0.316 951 -
all-1011 -
obs--96.29 %
Refinement TLS params.Method: refined / Origin x: 35.9356 Å / Origin y: -6.0581 Å / Origin z: 24.6465 Å
111213212223313233
T-0.395 Å20.1906 Å2-0.0045 Å2--0.3174 Å20.0522 Å2---0.328 Å2
L2.015 °22.3812 °2-1.521 °2-5.8988 °2-3.0545 °2--2.7265 °2
S-0.1372 Å °0.2274 Å °-0.1588 Å °-0.0852 Å °-0.1809 Å °-0.7764 Å °-0.0792 Å °0.2003 Å °0.3181 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-348 - 103
2X-RAY DIFFRACTION1B31 - 42
3X-RAY DIFFRACTION1A126

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