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- PDB-8gtm: Corticotropin-releasing hormone receptor 1(CRF1R) bound with BMK-... -

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Basic information

Entry
Database: PDB / ID: 8gtm
TitleCorticotropin-releasing hormone receptor 1(CRF1R) bound with BMK-C203 by XFEL
Components
  • EndolysinLysin
  • Isoform CRF-R2 of Corticotropin-releasing factor receptor 1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-0VI / Endolysin / Isoform CRF-R2 of Corticotropin-releasing factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T6 (virus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCho, H.S. / Kim, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Exp.Mol.Med. / Year: 2023
Title: Structure-based drug discovery of a corticotropin-releasing hormone receptor 1 antagonist using an X-ray free-electron laser.
Authors: Kim, H. / Lim, T. / Ha, G.E. / Lee, J.Y. / Kim, J.W. / Chang, N. / Kim, S.H. / Kim, K.H. / Lee, J. / Cho, Y. / Kim, B.W. / Abrahamsson, A. / Kim, S.H. / Kim, H.J. / Park, S. / Lee, S.J. / ...Authors: Kim, H. / Lim, T. / Ha, G.E. / Lee, J.Y. / Kim, J.W. / Chang, N. / Kim, S.H. / Kim, K.H. / Lee, J. / Cho, Y. / Kim, B.W. / Abrahamsson, A. / Kim, S.H. / Kim, H.J. / Park, S. / Lee, S.J. / Park, J. / Cheong, E. / Kim, B.M. / Cho, H.S.
History
DepositionSep 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform CRF-R2 of Corticotropin-releasing factor receptor 1
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3983
Polymers50,7992
Non-polymers5991
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-2 kcal/mol
Surface area22050 Å2
Unit cell
Length a, b, c (Å)95.660, 70.650, 86.750
Angle α, β, γ (deg.)90.000, 97.820, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Isoform CRF-R2 of Corticotropin-releasing factor receptor 1 / CRF-R-1 / CRF-R1 / CRFR-1 / Corticotropin-releasing hormone receptor 1 / CRH-R-1 / CRH-R1


Mass: 32685.355 Da / Num. of mol.: 1
Mutation: V120A, L144A, W156A, S160A, K228A, F260A, I277A, Y309A, F330A, S349A, Y363A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRHR1, CRFR, CRFR1, CRHR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34998-2
#2: Protein Endolysin / Lysin / Lysis protein / Lysozyme / Muramidase


Mass: 18113.703 Da / Num. of mol.: 1 / Mutation: C1052S, C1095S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T6 (virus) / Gene: e, EcT6_00117 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A346FJK3, lysozyme
#3: Chemical ChemComp-0VI / 7-(4-bromanyl-2,6-dimethoxy-phenyl)-4,8-dimethyl-~{N},~{N}-bis[4,4,4-tris(fluoranyl)butyl]-1$l^{4},3,5,9-tetrazabicyclo[4.3.0]nona-1(6),2,4,8-tetraen-2-amine


Mass: 599.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27BrF6N5O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.5
Details: 0.05M Na-Citrate(4.5), 0.06M NaCl 20~30% PEG 400(w/v)

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.278 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jan 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 2.6→56.64 Å / Num. obs: 18380 / % possible obs: 100 % / Redundancy: 113.8 % / Biso Wilson estimate: 63.33 Å2 / CC1/2: 0.9811 / R split: 0.1428 / Net I/σ(I): 4.87
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 1.25 / Num. unique obs: 1832 / CC1/2: 0.4896 / R split: 0.9935

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k5y

4k5y


Resolution: 2.6→56.64 Å / SU ML: 0.3299 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2602 521 2.93 %
Rwork0.2193 17255 -
obs0.2205 17776 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.47 Å2
Refinement stepCycle: LAST / Resolution: 2.6→56.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 37 0 3303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01223385
X-RAY DIFFRACTIONf_angle_d1.09644623
X-RAY DIFFRACTIONf_chiral_restr0.0873535
X-RAY DIFFRACTIONf_plane_restr0.0088570
X-RAY DIFFRACTIONf_dihedral_angle_d8.6624463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.860.31931280.29054272X-RAY DIFFRACTION99.91
2.86-3.280.25531290.23874291X-RAY DIFFRACTION99.91
3.28-4.130.26141310.21554310X-RAY DIFFRACTION100
4.13-56.640.25051330.20534382X-RAY DIFFRACTION99.98

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