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

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Basic information

Entry
Database: PDB / ID: 8enb
TitleCrystal structure of LGR ligand alpha2/beta5 from C. elegans in crystal form 2
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: 2.35 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 2.0Apr 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: atom_site / entity_poly ...atom_site / entity_poly / pdbx_contact_author / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
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.label_seq_id / _atom_site.type_symbol / _entity_poly.pdbx_strand_id / _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.pdbx_method_to_determine_struct / _software.classification / _software.name / _struct_asym.entity_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_label_asym_id / _struct_conf.end_auth_asym_id / _struct_conf.end_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Sequence discrepancy / Details: Macromolecule names were wrong. / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Bursicon
B: Cys_knot domain-containing protein
C: Bursicon
D: Cys_knot domain-containing protein


Theoretical massNumber of molelcules
Total (without water)44,3114
Polymers44,3114
Non-polymers00
Water73941
1
A: Bursicon
B: Cys_knot domain-containing protein


Theoretical massNumber of molelcules
Total (without water)22,1562
Polymers22,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Bursicon
D: Cys_knot domain-containing protein


Theoretical massNumber of molelcules
Total (without water)22,1562
Polymers22,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.371, 90.748, 59.563
Angle α, β, γ (deg.)90.000, 97.180, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_1ens_2chain "B"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNVALB1 - 87
d_21ens_1ASNVALA1 - 87
d_11ens_2GLUGLND1 - 101
d_21ens_2GLUGLNC1 - 101

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.647597214677, -0.559986666918, 0.516752146021), (-0.462641136245, -0.249901983415, -0.850595190287), (0.60545935173, -0.789913876039, -0.0972370394634)0.498650218225, -3.71566405786, 28.5604242367
2given(-0.590600136309, -0.662158923902, 0.461234255546), (-0.444557000043, -0.210035880093, -0.870777814822), (0.673469043613, -0.719326413091, -0.170320165349)3.48817342934, -4.63642220484, 27.1229509122

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Components

#1: Protein Bursicon / Bursicon subunit alpha


Mass: 10565.464 Da / Num. of mol.: 2
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: 11590.098 Da / Num. of mol.: 2
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
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: 3.17 Å3/Da / Density % sol: 61.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 12% w/v PEG6000

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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: Oct 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→49.52 Å / Num. obs: 15726 / % possible obs: 86.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 36.63 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.4
Reflection shellResolution: 2.3→2.47 Å / Num. unique obs: 787 / CC1/2: 0.264

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
PHENIX1.20rc3_4406refinement
XDSdata reduction
STARANISOdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→49.52 Å / SU ML: 0.3807 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.4177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2838 765 5 %
Rwork0.2384 14537 -
obs0.2407 15302 66.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.55 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 0 41 2957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342966
X-RAY DIFFRACTIONf_angle_d0.84153992
X-RAY DIFFRACTIONf_chiral_restr0.0476444
X-RAY DIFFRACTIONf_plane_restr0.0065524
X-RAY DIFFRACTIONf_dihedral_angle_d13.378398
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS1.27759184935
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS2.05210857402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.530.4391550.34521050X-RAY DIFFRACTION23.94
2.53-2.790.3621020.34031949X-RAY DIFFRACTION44.68
2.79-3.190.35241550.30192942X-RAY DIFFRACTION67.19
3.19-4.020.30992250.24944275X-RAY DIFFRACTION97.09
4.02-49.520.22092280.18874321X-RAY DIFFRACTION97.43

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