[English] 日本語
Yorodumi
- PDB-5vbl: Structure of apelin receptor in complex with agonist peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vbl
TitleStructure of apelin receptor in complex with agonist peptide
Components
  • Apelin receptor,Rubredoxin,Apelin receptor Chimera
  • agonist peptide
KeywordsMEMBRANE PROTEIN / human apelin receptor complex / agonist peptide / AMG3054 / GPCR / Rubredoxin / LCP / synchrotron radiation / peptide-GCPR recognition / cardiovascular drug target / specific recognition / binding specificity / designed agonist peptide mimic / ISOPEPTIDE
Function / homology
Function and homology information


apelin receptor activity / apelin receptor signaling pathway / regulation of gap junction assembly / positive regulation of inhibitory G protein-coupled receptor phosphorylation / vascular associated smooth muscle cell differentiation / atrioventricular valve development / regulation of body fluid levels / venous blood vessel development / alkane catabolic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...apelin receptor activity / apelin receptor signaling pathway / regulation of gap junction assembly / positive regulation of inhibitory G protein-coupled receptor phosphorylation / vascular associated smooth muscle cell differentiation / atrioventricular valve development / regulation of body fluid levels / venous blood vessel development / alkane catabolic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endocardial cushion formation / negative regulation of cAMP-mediated signaling / coronary vasculature development / adult heart development / vasculature development / aorta development / ventricular septum morphogenesis / blood vessel development / heart looping / vasculogenesis / gastrulation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / G protein-coupled receptor activity / positive regulation of angiogenesis / signaling receptor activity / heart development / G alpha (i) signalling events / regulation of gene expression / angiogenesis / electron transfer activity / iron ion binding / G protein-coupled receptor signaling pathway / negative regulation of gene expression / plasma membrane
Similarity search - Function
Apelin receptor / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / : ...Apelin receptor / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / : / 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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Rubredoxin / Apelin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMa, Y. / Yue, Y. / Ma, Y. / Zhang, Q. / Zhou, Q. / Song, Y. / Shen, Y. / Li, X. / Ma, X. / Li, C. ...Ma, Y. / Yue, Y. / Ma, Y. / Zhang, Q. / Zhou, Q. / Song, Y. / Shen, Y. / Li, X. / Ma, X. / Li, C. / Hanson, M.A. / Han, G.W. / Sickmier, E.A. / Swaminath, G. / Zhao, S. / Stevems, R.C. / Hu, L.A. / Zhong, W. / Zhang, M. / Xu, F.
CitationJournal: Structure / Year: 2017
Title: Structural Basis for Apelin Control of the Human Apelin Receptor
Authors: Ma, Y. / Yue, Y. / Ma, Y. / Zhang, Q. / Zhou, Q. / Song, Y. / Shen, Y. / Li, X. / Ma, X. / Li, C. / Hanson, M.A. / Han, G.W. / Sickmier, E.A. / Swaminath, G. / Zhao, S. / Stevens, R.C. / Hu, ...Authors: Ma, Y. / Yue, Y. / Ma, Y. / Zhang, Q. / Zhou, Q. / Song, Y. / Shen, Y. / Li, X. / Ma, X. / Li, C. / Hanson, M.A. / Han, G.W. / Sickmier, E.A. / Swaminath, G. / Zhao, S. / Stevens, R.C. / Hu, L.A. / Zhong, W. / Zhang, M. / Xu, F.
History
DepositionMar 29, 2017Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Jun 30, 2021Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.3Nov 8, 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 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: agonist peptide
B: Apelin receptor,Rubredoxin,Apelin receptor Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2494
Polymers48,8272
Non-polymers4222
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-17 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.580, 44.300, 79.450
Angle α, β, γ (deg.)90.00, 114.87, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein/peptide agonist peptide


Mass: 2383.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Apelin receptor,Rubredoxin,Apelin receptor Chimera / Angiotensin receptor-like 1 / G-protein coupled receptor APJ / G-protein coupled receptor HG11 / Rd


Mass: 46443.621 Da / Num. of mol.: 1
Fragment: UNP residues 7-229, UNP residues 1-54, UNP residues 243-330
Mutation: V117A, T177N,W261K, C325L, C326M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: APLNR, AGTRL1, APJ / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35414, UniProt: P00268
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100mM MES pH 6.1, 26% PEG500 DME, 125mM MgCl2, 100mM NaCl, 500uM AMG3054

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→41.61 Å / Num. obs: 13686 / % possible obs: 91.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 54.49 Å2 / Net I/σ(I): 6.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.488 / % possible all: 88.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EJ4

4ej4


Resolution: 2.6→41.61 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.865 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.799 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.721 / SU Rfree Blow DPI: 0.308 / SU Rfree Cruickshank DPI: 0.317
RfactorNum. reflection% reflectionSelection details
Rfree0.256 686 5.01 %RANDOM
Rwork0.239 ---
obs0.24 13686 91.6 %-
Displacement parametersBiso mean: 63.57 Å2
Baniso -1Baniso -2Baniso -3
1--3.3238 Å20 Å2-3.7033 Å2
2---10.2815 Å20 Å2
3---13.6053 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: 1 / Resolution: 2.6→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2878 0 71 4 2953
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083034HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.874132HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d998SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes451HARMONIC5
X-RAY DIFFRACTIONt_it3034HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.62
X-RAY DIFFRACTIONt_other_torsion19.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion396SEMIHARMONIC5
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_contact3369SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.232 124 4.6 %
Rwork0.233 2569 -
all0.233 2693 -
obs--88.87 %
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)
10.67-1.2314-0.03140-0.03511.3396-0.0044-0.01060.01190.01090-0.0095-0.0057-0.00850.0044-0.015-0.00580.02520.0522-0.0236-0.0119191.2978-8.745363.5302
21.32320.423-0.17861.14960.37982.97830.0005-0.06880.01670.0387-0.0246-0.0814-0.02210.00240.024-0.17350.05660.0050.05040.0019-0.1991189.2486-8.017337.708
30.2141.7297-0.49791.54210.50322.06970.0184-0.0206-0.00750.0212-0.00460.0569-0.0031-0.0211-0.01380.1846-0.04820.02640.0453-0.0658-0.2181184.8994-31.4301-0.6365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|17}
2X-RAY DIFFRACTION2{ B|19 - B|229 or B|243 - B|330}
3X-RAY DIFFRACTION3{ B|1001 - B|1054 }

+
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://pdbjlc1.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