[English] 日本語
Yorodumi
- PDB-6kk7: Structure of thermal-stabilised(M6) human GLP-1 receptor transmem... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kk7
TitleStructure of thermal-stabilised(M6) human GLP-1 receptor transmembrane domain
ComponentsGlucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptor
KeywordsSIGNALING PROTEIN / GPCR / seven-transmembrane / allosteric modulators / diabetes
Function / homology
Function and homology information


glucagon-like peptide 1 receptor activity / glucagon receptor activity / positive regulation of blood pressure / hormone secretion / post-translational protein targeting to membrane, translocation / response to psychosocial stress / regulation of heart contraction / peptide hormone binding / viral release from host cell by cytolysis / activation of adenylate cyclase activity ...glucagon-like peptide 1 receptor activity / glucagon receptor activity / positive regulation of blood pressure / hormone secretion / post-translational protein targeting to membrane, translocation / response to psychosocial stress / regulation of heart contraction / peptide hormone binding / viral release from host cell by cytolysis / activation of adenylate cyclase activity / negative regulation of blood pressure / peptidoglycan catabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / lysozyme / lysozyme activity / transmembrane signaling receptor 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. / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-97Y / Endolysin / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSong, G.
CitationJournal: Iucrj / Year: 2019
Title: Mutagenesis facilitated crystallization of GLP-1R.
Authors: Xu, Y. / Wang, Y. / Wang, Y. / Liu, K. / Peng, Y. / Yao, D. / Tao, H. / Liu, H. / Song, G.
History
DepositionJul 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.pdbx_database_id_PubMed ..._audit_author.name / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,1304
Polymers105,0982
Non-polymers1,0312
Water00
1
A: Glucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0652
Polymers52,5491
Non-polymers5161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0652
Polymers52,5491
Non-polymers5161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.230, 71.060, 81.000
Angle α, β, γ (deg.)92.48, 92.61, 105.10
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 52549.227 Da / Num. of mol.: 2
Mutation: S225A,I317C,G318I,K346A,C347F,G361C,205-214deletion,R1011G,C1053T,C1096A,I1136R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: GLP1R / Plasmid: pfasctbac / Cell (production host): SF9 / Cell line (production host): IPLB-Sf-21-AE
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P43220, UniProt: P00720
#2: Chemical ChemComp-97Y / N-{4-[(R)-(3,3-dimethylcyclobutyl)({6-[4-(trifluoromethyl)-1H-imidazol-1-yl]pyridin-3-yl}amino)methyl]benzene-1-carbonyl}-beta-alanine


Mass: 515.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28F3N5O3
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.4-0.45 M ammonium acetate, 0.1 M sodium cacodylate, pH 6.2-6.6, 35-38% PEG400, 3% w/v aminohexanoic acid

-
Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→41.2 Å / Num. obs: 20302 / % possible obs: 79.9 % / Redundancy: 2.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.6
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2761 / CC1/2: 0.61 / % possible all: 74.5

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VEW

5vew


Resolution: 3.1→40.392 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 39.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3032 955 4.72 %
Rwork0.2568 19263 -
obs0.2589 20218 79.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 266.65 Å2 / Biso mean: 104.4108 Å2 / Biso min: 37.02 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 74 0 6664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136825
X-RAY DIFFRACTIONf_angle_d1.5579295
X-RAY DIFFRACTIONf_chiral_restr0.0851085
X-RAY DIFFRACTIONf_plane_restr0.0091132
X-RAY DIFFRACTIONf_dihedral_angle_d4.9323932
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1001-3.26340.53061360.44422525266173
3.2634-3.46780.39071450.35332700284579
3.4678-3.73540.30061350.30022739287479
3.7354-4.11090.31841650.2662847301283
4.1109-4.7050.27721390.22742806294581
4.705-5.92480.29551220.24092905302783
5.9248-40.39520.23491130.20682741285479
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)
14.4940.1224-3.08431.2808-0.68353.73830.0320.7402-0.524-0.1901-0.3115-0.19410.70140.0498-0.09180.86720.0787-0.03230.7879-0.0720.685711.7186-40.0325-47.1605
21.9420.0732-0.00662.7056-0.22864.61790.14071.0666-1.13870.0288-0.09250.61480.33661.0834-0.23720.8962-0.1051-0.0354-0.5187-0.12340.80562.1522-34.4071-39.6093
31.6711-0.1464-0.00492.39371.26511.73280.21891.59870.7739-0.5813-0.80370.5326-0.04040.01110.16550.5708-0.4375-0.1776-1.7397-0.48550.47783.1924-25.7883-46.9925
41.1709-0.02590.39712.4222-0.31780.26190.3551-1.30840.51340.23870.24970.3598-0.69340.3009-0.33290.7178-0.14610.17081.3335-0.20630.8379-0.982-18.707-48.661
53.3327-0.85610.02581.8552-0.09163.09790.1263-0.81470.20750.17640.371-0.01210.02590.3296-0.13170.5462-0.02060.02261.02420.10670.494614.652-19.129-35.715
62.10871.3360.12282.5799-2.02282.7640.0645-0.42960.07420.37891.25480.36740.5078-0.6771-0.20930.2352-0.52950.17872.01770.36630.806714.378-34.514-38.543
71.37190.0013-0.15031.2479-0.09234.5854-0.04290.3082-0.1116-0.1877-0.1555-0.0413-0.42020.04330.08810.40.05280.01250.58250.05420.47934.152-50.509-19.612
83.4428-0.87143.41231.8527-2.17026.38770.36940.51520.3003-0.0098-0.07770.12440.83820.9627-0.12470.44290.05130.11980.50440.06250.5186-5.775-10.053-3.342
91.62550.0273-0.59691.628-0.19072.0021-0.0104-0.5645-0.0512-0.2178-0.0482-0.04540.05520.70250.14810.59160.0462-0.02390.6325-0.07160.7383.107-12.638-1.128
104.76751.65740.14327.62180.44244.25110.5138-0.3793-0.30571.03120.21430.10411.35760.1616-0.22411.5016-0.02740.17541.5946-0.01221.348-3.627-29.982-6.484
112.96511.33511.86371.21391.19524.33710.2242-0.29770.003-0.04570.4163-0.7207-0.64870.0781-0.33890.8235-0.22110.13421.2112-0.60841.268845.67084.788-36.0783
121.9568-0.44910.07491.7908-0.55581.85610.1896-0.42430.34840.1039-0.07560.2386-0.39040.7392-0.13750.53290.00820.03730.5596-0.10260.561336.3167-5.2934-40.8685
131.76571.05731.02592.50140.45691.57620.20730.770.0214-0.57780.02440.3490.5266-0.1714-0.17820.87580.1183-0.19261.0201-0.10040.875331.417-16.035-35.132
143.90792.65640.87029.0931.36172.24350.05860.5835-1.1581-0.8032-0.0044-0.73980.67940.2287-0.44910.80020.1524-0.03891.1249-0.24660.890445.093-20.249-45.487
151.4-0.0077-0.44312.1828-0.03012.50120.32360.7652-0.1919-0.59150.0475-0.0354-0.750.974-0.19680.480.02450.03941.18920.1140.544149.877-10.711-57.915
163.339-0.43060.78071.1239-0.04591.02250.13730.27330.5592-0.1775-0.06760.6731-0.3834-0.3449-0.05260.90260.00220.00291.81150.18020.736150.938-9.418-34.104
172.61930.2468-0.63923.706-2.33414.1746-0.2548-0.52820.46430.25170.33920.15180.1146-0.36530.05670.4999-0.0099-0.03580.89430.24050.691446.571-58.935
181.52050.6294-0.50641.137-0.82862.10220.0913-1.13480.2520.3522-0.44280.0138-0.55610.06990.08860.55350.03190.03331.1568-0.13890.577939.37622.277-64.341
193.88480.6785-2.31912.3012-2.21353.89930.068-0.43580.10240.11030.0732-0.0217-0.32970.6887-0.05640.5047-0.0823-0.00790.3498-0.06540.64829.544-24.566-80.447
202.48820.29560.152.24850.70840.557-0.27981.51930.26230.17920.6378-0.1625-0.5042-0.35980.11040.45940.32210.0344-0.02490.17710.615132.376-34.81-86.043
210.53720.3640.08352.01440.55750.0121-0.78630.42-0.21910.39920.1126-1.4285-0.12280.06470.38180.7330.0321-0.06061.3025-0.1920.922943.726-13.06-79.654
221.7555-3.88721.43528.3381-3.55421.55590.0720.77570.326-0.8714-0.0296-0.0145-1.0946-0.49410.12191.56410.0792-0.04941.1235-0.01570.836433.19-4.904-77.406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 136:168 )A136 - 168
2X-RAY DIFFRACTION2( CHAIN A AND RESID 169:201 )A169 - 201
3X-RAY DIFFRACTION3( CHAIN A AND RESID 202:256 )A202 - 256
4X-RAY DIFFRACTION4( CHAIN A AND RESID 257:304 )A257 - 304
5X-RAY DIFFRACTION5( CHAIN A AND RESID 305:381 )A305 - 381
6X-RAY DIFFRACTION6( CHAIN A AND RESID 382:411 )A382 - 411
7X-RAY DIFFRACTION7( CHAIN A AND RESID 412:422 )A412 - 422
8X-RAY DIFFRACTION8( CHAIN A AND RESID 1001:1033 )A1001 - 1033
9X-RAY DIFFRACTION9( CHAIN A AND RESID 1034:1099 )A1034 - 1099
10X-RAY DIFFRACTION10( CHAIN A AND RESID 1100:1160 )A1100 - 1160
11X-RAY DIFFRACTION11( CHAIN B AND RESID 136:168 )B136 - 168
12X-RAY DIFFRACTION12( CHAIN B AND RESID 169:256 )B169 - 256
13X-RAY DIFFRACTION13( CHAIN B AND RESID 257:304 )B257 - 304
14X-RAY DIFFRACTION14( CHAIN B AND RESID 305:335 )B305 - 335
15X-RAY DIFFRACTION15( CHAIN B AND RESID 336:361 )B336 - 361
16X-RAY DIFFRACTION16( CHAIN B AND RESID 362:398 )B362 - 398
17X-RAY DIFFRACTION17( CHAIN B AND RESID 399:419 )B399 - 419
18X-RAY DIFFRACTION18( CHAIN B AND RESID 420:422 )B420 - 422
19X-RAY DIFFRACTION19( CHAIN B AND RESID 1001:1033 )B1001 - 1033
20X-RAY DIFFRACTION20( CHAIN B AND RESID 1034:1063 )B1034 - 1063
21X-RAY DIFFRACTION21( CHAIN B AND RESID 1064:1098 )B1064 - 1098
22X-RAY DIFFRACTION22( CHAIN B AND RESID 1099:1160 )B1099 - 1160

+
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