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- PDB-8end: Crystal structure of LGR ligand alpha2/beta5 from C. elegans in c... -

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Basic information

Entry
Database: PDB / ID: 8end
TitleCrystal structure of LGR ligand alpha2/beta5 from C. elegans in crystal form 1 (SeMet)
Components
  • Bursicon
  • Cys_knot domain-containing protein
KeywordsSTRUCTURAL PROTEIN / cystine-knot hormone (CKH) / leucine-rich repeat-containing G protein-coupled receptor (LGR) / evolution / glycoprotein hormone (GPH) / thyrostimulin
Function / homology
Function and homology information


Hormone ligand-binding receptors / G alpha (s) signalling events / hormone activity / G protein-coupled receptor signaling pathway / extracellular space / extracellular region / cytoplasm
Similarity search - Function
: / DAN / DAN domain / Gonadotropin, beta subunit / Glycoprotein hormone subunit beta / Cystine-knot domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines ...: / DAN / DAN domain / Gonadotropin, beta subunit / Glycoprotein hormone subunit beta / Cystine-knot domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Glycoprotein hormone alpha 2 / Glycoprotein hormone subunit beta domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.54 Å
AuthorsGong, Z. / Hendrickson, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107462 United States
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2023
Title: Crystal structure of LGR ligand alpha2/beta5 from Caenorhabditis elegans with implications for the evolution of glycoprotein hormones
Authors: Gong, Z. / Wang, W. / El Omari, K. / Lebedev, A.A. / Clarke, O.B. / Hendrickson, W.A.
#1: Journal: To be Published
Title: Combining AlphaFold and phenix.mr_rosetta for solving challenging crystal structures
Authors: Wang, W. / Gong, Z. / Hendrickson, W.A.
History
DepositionSep 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Refinement description / Structure summary
Category: pdbx_contact_author / pdbx_initial_refinement_model ...pdbx_contact_author / pdbx_initial_refinement_model / refine / software
Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name ..._pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bursicon
B: Cys_knot domain-containing protein


Theoretical massNumber of molelcules
Total (without water)22,3902
Polymers22,3902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-21 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.530, 92.530, 95.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Bursicon / Bursicon subunit alpha


Mass: 10706.149 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Homo sapiens (human) / References: UniProt: A0T3A2
#2: Protein Cys_knot domain-containing protein / Putative glycoprotein hormone-beta5


Mass: 11683.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gpb5, CELE_T23B12.8, T23B12.8 / Production host: Homo sapiens (human) / References: UniProt: A7DT38
Has ligand of interestN
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: 5.28 Å3/Da / Density % sol: 76.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M MES, pH 6.0, 40% w/v PEG200, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.54→49.03 Å / Num. obs: 4990 / % possible obs: 92.8 % / Redundancy: 494 % / Biso Wilson estimate: 171.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.455 / Net I/σ(I): 21
Reflection shellResolution: 3.54→3.89 Å / Num. unique obs: 413 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
XDSdata reduction
STARANISOdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8ENB

8enb


Resolution: 3.54→46.27 Å / SU ML: 0.4615 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 42.3133
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3295 509 10.2 %
Rwork0.2819 4480 -
obs0.2864 4989 82.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 184.97 Å2
Refinement stepCycle: LAST / Resolution: 3.54→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 0 0 1505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321532
X-RAY DIFFRACTIONf_angle_d0.72132061
X-RAY DIFFRACTIONf_chiral_restr0.0494227
X-RAY DIFFRACTIONf_plane_restr0.0056271
X-RAY DIFFRACTIONf_dihedral_angle_d5.9106205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.54-3.890.4189460.4127365X-RAY DIFFRACTION27.77
3.89-4.460.33571510.31251345X-RAY DIFFRACTION99.67
4.46-5.610.37111480.33531347X-RAY DIFFRACTION100
5.61-46.270.31051640.25111423X-RAY DIFFRACTION99.94

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