[English] 日本語
Yorodumi
- PDB-8enb: Crystal structure of LGR ligand alpha2/beta5 from C. elegans in c... -

+
Open data


ID or keywords:

Loading...

-
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 cytokine
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more