[English] 日本語
Yorodumi
- PDB-5otw: Extracellular domain of GLP-1 receptor in complex with GLP-1 vari... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5otw
TitleExtracellular domain of GLP-1 receptor in complex with GLP-1 variant Ala8Hcs/Thr11Cys
Components
  • Glucagon
  • Glucagon-like peptide 1 receptor
KeywordsSIGNALING PROTEIN / glucagon-like peptide 1 / GPCR / cyclic peptides
Function / homology
Function and homology information


glucagon receptor binding / glucagon-like peptide 1 receptor activity / glucagon receptor activity / : / positive regulation of blood pressure / hormone secretion / post-translational protein targeting to membrane, translocation / negative regulation of execution phase of apoptosis / feeding behavior / response to psychosocial stress ...glucagon receptor binding / glucagon-like peptide 1 receptor activity / glucagon receptor activity / : / positive regulation of blood pressure / hormone secretion / post-translational protein targeting to membrane, translocation / negative regulation of execution phase of apoptosis / feeding behavior / response to psychosocial stress / regulation of heart contraction / positive regulation of calcium ion import / peptide hormone binding / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of insulin secretion involved in cellular response to glucose stimulus / activation of adenylate cyclase activity / negative regulation of blood pressure / positive regulation of gluconeogenesis / cellular response to glucagon stimulus / regulation of insulin secretion / response to activity / gluconeogenesis / hormone activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / transmembrane signaling receptor activity / glucose homeostasis / positive regulation of cytosolic calcium ion concentration / secretory granule lumen / G alpha (s) signalling events / G alpha (q) signalling events / learning or memory / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Glucagon / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / GPCR, family 2, glucagon-like peptide-1 receptor / : / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / GPCR, family 2, glucagon-like peptide-1/glucagon receptor ...Glucagon / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / GPCR, family 2, glucagon-like peptide-1 receptor / : / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / 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. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Pro-glucagon / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMortensen, S.
CitationJournal: Biochemistry / Year: 2018
Title: alpha-Helix or beta-Turn? An Investigation into N-Terminally Constrained Analogues of Glucagon-like Peptide 1 (GLP-1) and Exendin-4.
Authors: Oddo, A. / Mortensen, S. / Thogersen, H. / De Maria, L. / Hennen, S. / McGuire, J.N. / Kofoed, J. / Linderoth, L. / Reedtz-Runge, S.
History
DepositionAug 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Mar 6, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Glucagon-like peptide 1 receptor
D: Glucagon
A: Glucagon-like peptide 1 receptor
B: Glucagon


Theoretical massNumber of molelcules
Total (without water)33,9114
Polymers33,9114
Non-polymers00
Water2,432135
1
C: Glucagon-like peptide 1 receptor
D: Glucagon


Theoretical massNumber of molelcules
Total (without water)16,9562
Polymers16,9562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-11 kcal/mol
Surface area8080 Å2
MethodPISA
2
A: Glucagon-like peptide 1 receptor
B: Glucagon


Theoretical massNumber of molelcules
Total (without water)16,9562
Polymers16,9562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-10 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.260, 81.200, 42.740
Angle α, β, γ (deg.)90.00, 98.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glucagon-like peptide 1 receptor / GLP-1R


Mass: 13547.892 Da / Num. of mol.: 2 / Fragment: extracellular domain, UNP residues 24-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLP1R / Production host: Escherichia coli (E. coli) / References: UniProt: P43220
#2: Protein/peptide Glucagon


Mass: 3407.830 Da / Num. of mol.: 2 / Mutation: A8HCS, T11C / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01275
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus from Molecular Dimensions, solution E12: 0.12 M ethylene Glycols, 0.1 M Buffer system 3 pH 8.5, 12.5% (v/v) MPD, 12.5% (w/v) PEG1000, 12.5% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Feb 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.1→42.26 Å / Num. obs: 15304 / % possible obs: 98.5 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.049 / Rsym value: 0.118 / Net I/σ(I): 11.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.53 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.9 / Num. measured obs: 4245 / Num. unique all: 767 / CC1/2: 0.742 / Rpim(I) all: 0.459 / Rrim(I) all: 1.086 / % possible all: 95.64

-
Processing

Software
NameVersionClassification
PHENIX(dev_2689: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZGM

4zgm


Resolution: 2.1→42.252 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.54
RfactorNum. reflection% reflection
Rfree0.2392 2796 9.36 %
Rwork0.1839 --
obs0.189 15288 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 0 135 2207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052150
X-RAY DIFFRACTIONf_angle_d0.7232936
X-RAY DIFFRACTIONf_dihedral_angle_d10.6841231
X-RAY DIFFRACTIONf_chiral_restr0.042291
X-RAY DIFFRACTIONf_plane_restr0.006377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13620.38961220.29771343X-RAY DIFFRACTION94
2.1362-2.17510.26661200.25251330X-RAY DIFFRACTION97
2.1751-2.21690.32551610.25081335X-RAY DIFFRACTION98
2.2169-2.26210.37891540.27191319X-RAY DIFFRACTION96
2.2621-2.31130.33821280.23141394X-RAY DIFFRACTION97
2.3113-2.36510.28321300.21431283X-RAY DIFFRACTION98
2.3651-2.42420.25371430.20061370X-RAY DIFFRACTION98
2.4242-2.48980.28511470.22031366X-RAY DIFFRACTION97
2.4898-2.5630.24081220.2011333X-RAY DIFFRACTION97
2.563-2.64570.33831450.20621346X-RAY DIFFRACTION98
2.6457-2.74030.22051350.18481352X-RAY DIFFRACTION99
2.7403-2.850.24761410.19541418X-RAY DIFFRACTION99
2.85-2.97960.24711410.18731383X-RAY DIFFRACTION100
2.9796-3.13670.27851360.19691351X-RAY DIFFRACTION99
3.1367-3.33310.23211540.16621365X-RAY DIFFRACTION100
3.3331-3.59040.19991340.14821379X-RAY DIFFRACTION99
3.5904-3.95140.22921460.15151344X-RAY DIFFRACTION99
3.9514-4.52270.16531400.15351356X-RAY DIFFRACTION98
4.5227-5.69590.1711440.15281342X-RAY DIFFRACTION98
5.6959-42.26060.2331530.17731377X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8546-0.16280.72281.44780.12155.88220.03990.04930.0114-0.08710.0407-0.0442-0.07990.1686-0.0940.17350.00130.01380.133-0.01650.168338.46947.64156.133
20.95980.368-0.86174.2344-5.26736.7198-0.24280.0837-0.25950.1710.2227-0.2224-0.2418-0.2938-0.15560.2445-0.01750.02980.2805-0.00310.263429.014-2.42925.8497
33.65860.5676-1.95382.1670.23465.65620.0458-0.06070.0351-0.09940.0140.04360.02490.0117-0.0390.19550.0009-0.00540.14790.0130.17456.1492-11.77742.6235
42.9661.04821.49287.21734.29657.9542-0.16910.01410.13470.21260.24460.1460.15130.1221-0.15380.1729-0.02220.00070.23680.01430.193359.4444-3.453123.6755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 29 through 128)
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 35)
3X-RAY DIFFRACTION3(chain 'C' and resid 29 through 128)
4X-RAY DIFFRACTION4(chain 'D' and resid 10 through 35)

+
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