[English] 日本語
Yorodumi
- PDB-5vex: Structure of the human GLP-1 receptor complex with NNC0640 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vex
TitleStructure of the human GLP-1 receptor complex with NNC0640
ComponentsGlucagon-like peptide 1 receptor, Endolysin chimera
KeywordsSIGNALING PROTEIN / GPCR / class B / 7TM domain / treatment of type 2 diabetes
Function / homology
Function and homology information


glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / regulation of heart contraction / response to psychosocial stress / peptide hormone binding / activation of adenylate cyclase activity / viral release from host cell by cytolysis ...glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / regulation of heart contraction / response to psychosocial stress / peptide hormone binding / activation of adenylate cyclase activity / viral release from host cell by cytolysis / negative regulation of blood pressure / cAMP-mediated signaling / peptidoglycan catabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / transmembrane signaling receptor activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / host cell cytoplasm / learning or memory / cell surface receptor signaling pathway / defense response to bacterium / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, glucagon-like peptide-1 receptor / : / 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 ...GPCR, family 2, glucagon-like peptide-1 receptor / : / 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. / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-97V / Endolysin / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSong, G. / Yang, D. / Wang, Y. / Graaf, C.D. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. ...Song, G. / Yang, D. / Wang, Y. / Graaf, C.D. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. / Liu, D. / Wu, F. / Wu, Y. / Zhao, S. / Ye, L. / Han, G.W. / Lau, J. / Wu, B. / Hanson, M.A. / Liu, Z.-J. / Wang, M.-W. / Stevens, R.C.
CitationJournal: Nature / Year: 2017
Title: Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators.
Authors: Song, G. / Yang, D. / Wang, Y. / de Graaf, C. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. / Liu, D. / Wu, F. / Wu, Y. / Zhao, S. / Ye, L. / Han, G.W. / Lau, J. / Wu, B. / ...Authors: Song, G. / Yang, D. / Wang, Y. / de Graaf, C. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. / Liu, D. / Wu, F. / Wu, Y. / Zhao, S. / Ye, L. / Han, G.W. / Lau, J. / Wu, B. / Hanson, M.A. / Liu, Z.J. / Wang, M.W. / Stevens, R.C.
History
DepositionApr 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucagon-like peptide 1 receptor, Endolysin chimera
B: Glucagon-like peptide 1 receptor, Endolysin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3224
Polymers105,1752
Non-polymers1,1472
Water00
1
A: Glucagon-like peptide 1 receptor, Endolysin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1612
Polymers52,5871
Non-polymers5741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucagon-like peptide 1 receptor, Endolysin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1612
Polymers52,5871
Non-polymers5741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.810, 67.510, 83.660
Angle α, β, γ (deg.)91.55, 89.88, 107.56
Int Tables number1
Space group name H-MP1
DetailsTHE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

-
Components

#1: Protein Glucagon-like peptide 1 receptor, Endolysin chimera / GLP-1R / Lysis protein / Lysozyme / Muramidase


Mass: 52587.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: GLP1R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43220, UniProt: P00720, lysozyme
#2: Chemical ChemComp-97V / 4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl)phenyl]carbamoyl}amino]methyl}-N-(1H-tetrazol-5-yl)benzamide


Mass: 573.666 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H31N7O4S
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.4-0.45 M ammonium acetate, 0.1 M sodium acetate, pH 5.0-5.8, 38-40% PEG400

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 24745 / % possible obs: 91.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 92.82 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.6 / CC1/2: 0.66 / % possible all: 87.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 5ee7 and 212L
Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.389
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1060 4.29 %RANDOM
Rwork0.233 ---
obs0.234 24728 91.4 %-
Displacement parametersBiso mean: 111.74 Å2
Baniso -1Baniso -2Baniso -3
1-11.7226 Å2-1.9677 Å2-0.6183 Å2
2---27.3262 Å23.1345 Å2
3---15.6036 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: 1 / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6609 0 98 0 6707
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016877HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.869372HARMONIC2.5
X-RAY DIFFRACTIONt_dihedral_angle_d3056SINUSOIDAL15
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1015HARMONIC5
X-RAY DIFFRACTIONt_it6877HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion1.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion910SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8120SEMIHARMONIC4
LS refinement shellResolution: 3→3.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.289 135 4.6 %
Rwork0.243 2801 -
all0.245 2936 -
obs--87.76 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.46190.1438-0.37741.0720.21664.49360.2313-0.2453-0.03920.07610.00780.120.54380.0765-0.2391-0.3862-0.0781-0.01650.1968-0.0359-0.39966.2031-22.8618-27.7299
21.9858-0.03050.98911.22240.20774.07450.19150.18550.2117-0.0524-0.0660.1148-0.47030.0496-0.1255-0.43680.00890.06450.228-0.0246-0.382838.558-10.2411-58.0396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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