[English] 日本語
Yorodumi
- PDB-8s4d: Crystal structure of a peptidergic GPCR in complex with a small s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8s4d
TitleCrystal structure of a peptidergic GPCR in complex with a small synthetic G protein-biased agonist
ComponentsApelin receptor,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / receptor / GPCR / stabilised
Function / homology
Function and homology information


apelin receptor activity / apelin receptor signaling pathway / mechanoreceptor activity / regulation of gap junction assembly / positive regulation of G protein-coupled receptor internalization / vascular associated smooth muscle cell differentiation / atrioventricular valve development / regulation of body fluid levels / venous blood vessel development / positive regulation of cardiac muscle hypertrophy in response to stress ...apelin receptor activity / apelin receptor signaling pathway / mechanoreceptor activity / regulation of gap junction assembly / positive regulation of G protein-coupled receptor internalization / vascular associated smooth muscle cell differentiation / atrioventricular valve development / regulation of body fluid levels / venous blood vessel development / positive regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cAMP-mediated signaling / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endocardial cushion formation / coronary vasculature development / vasculature development / adult heart development / G protein-coupled peptide receptor activity / aorta development / negative regulation of cardiac muscle hypertrophy in response to stress / ventricular septum morphogenesis / blood vessel development / heart looping / vasculogenesis / gastrulation / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / electron transport chain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / positive regulation of angiogenesis / signaling receptor activity / heart development / regulation of gene expression / G alpha (i) signalling events / angiogenesis / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / negative regulation of gene expression / heme binding / plasma membrane
Similarity search - Function
Apelin receptor / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
: / OLEIC ACID / Soluble cytochrome b562 / Apelin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli O139:H28 str. E24377A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.584 Å
AuthorsVerdon, G. / Currinn, H. / Solcan, N. / Schlenker, O. / Brown, A.J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateRG86507 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Structural and functional determination of peptide versus small molecule ligand binding at the apelin receptor.
Authors: Williams, T.L. / Verdon, G. / Kuc, R.E. / Currinn, H. / Bender, B. / Solcan, N. / Schlenker, O. / Macrae, R.G.C. / Brown, J. / Schutz, M. / Zhukov, A. / Sinha, S. / de Graaf, C. / Graf, S. / ...Authors: Williams, T.L. / Verdon, G. / Kuc, R.E. / Currinn, H. / Bender, B. / Solcan, N. / Schlenker, O. / Macrae, R.G.C. / Brown, J. / Schutz, M. / Zhukov, A. / Sinha, S. / de Graaf, C. / Graf, S. / Maguire, J.J. / Brown, A.J.H. / Davenport, A.P.
History
DepositionFeb 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apelin receptor,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6469
Polymers56,2581
Non-polymers2,3898
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-9 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.823, 153.948, 111.646
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Apelin receptor,Soluble cytochrome b562 / Angiotensin receptor-like 1 / G-protein coupled receptor APJ / G-protein coupled receptor HG11


Mass: 56257.812 Da / Num. of mol.: 1
Mutation: T87V,N112A,T177N,T207M,F214L,I224A,S298A,C325L,C326M
Source method: isolated from a genetically manipulated source
Details: apelin receptor with bRIL fusion inserted in ICL3,apelin receptor with bRIL fusion inserted in ICL3,apelin receptor with bRIL fusion inserted in ICL3
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli O139:H28 str. E24377A (bacteria)
Gene: APLNR, AGTRL1, APJ, cybC, EcE24377A_4806 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35414, UniProt: A7ZVB5
#2: Chemical ChemComp-A1D5N / (3~{S})-5-methyl-3-[[1-pentan-3-yl-2-(thiophen-2-ylmethyl)benzimidazol-5-yl]carbonylamino]hexanoic acid / CMF019


Mass: 455.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H33N3O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.07 % / Description: rods
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.75
Details: 25 to 35 % polyethylene glycol (PEG) 400, 100 mM sodium citrate, pH 4.75, and 150 mM of ammonium phosphate or ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.58→76.97 Å / Num. obs: 9698 / % possible obs: 90.1 % / Redundancy: 14.8 % / CC1/2: 0.923 / Rpim(I) all: 0.145 / Net I/σ(I): 7.1
Reflection shellResolution: 2.58→2.929 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 223 / CC1/2: 0.497

-
Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
Cootmodel building
GDAdata collection
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.584→76.97 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.485
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 481 -RANDOM
Rwork0.2321 ---
obs0.2344 9705 53.4 %-
Displacement parametersBiso mean: 65.57 Å2
Baniso -1Baniso -2Baniso -3
1--6.7372 Å20 Å20 Å2
2---3.5527 Å20 Å2
3---10.2899 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.584→76.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 105 2 3131
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083203HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.924333HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1090SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes511HARMONIC5
X-RAY DIFFRACTIONt_it3203HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion411SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2624SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion21.77
LS refinement shellResolution: 2.584→3.03 Å /
RfactorNum. reflection
Rfree0.33 16
Rwork0.2743 -
Refinement TLS params.

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)
11.63280.35960.10341.30540.92450.64150.00870.03560.00080.03560.04040.03090.00080.0309-0.0491-0.11010.01140.0244-0.09970.06090.0221-3.6461-39.89732.0897
27.6989-0.52361.9980.52390.0344.22190.0551-0.28230.0328-0.2823-0.1699-0.04130.0328-0.04130.1149-0.00340.0514-0.0457-0.27150.0461-0.0513-16.7315-75.8377-27.822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|28 - A|328 B|1 - B|1 }A29 - 228
2X-RAY DIFFRACTION1{ A|28 - A|328 B|1 - B|1 }A235 - 324
3X-RAY DIFFRACTION1{ A|28 - A|328 B|1 - B|1 }B1
4X-RAY DIFFRACTION2{ A|1001 - A|1106 }A1001 - 1106

+
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