[English] 日本語
Yorodumi
- PDB-6ibb: Crystal structure of the rat isoform of the succinate receptor SU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ibb
TitleCrystal structure of the rat isoform of the succinate receptor SUCNR1 (GPR91) in complex with a nanobody
Components
  • Nanobody6
  • Succinate receptor 1
KeywordsMEMBRANE PROTEIN / SUCNR1 GPR91 GPCR G-Protein coupled receptor Nanobody Succinate Complex
Function / homology
Function and homology information


Class A/1 (Rhodopsin-like receptors) / regulation of angiotensin metabolic process / renin secretion into blood stream / positive regulation of chemotaxis / macrophage activation involved in immune response / G alpha (i) signalling events / energy homeostasis / G protein-coupled receptor activity / positive regulation of inflammatory response / response to calcium ion ...Class A/1 (Rhodopsin-like receptors) / regulation of angiotensin metabolic process / renin secretion into blood stream / positive regulation of chemotaxis / macrophage activation involved in immune response / G alpha (i) signalling events / energy homeostasis / G protein-coupled receptor activity / positive regulation of inflammatory response / response to calcium ion / glucose homeostasis / signaling receptor activity / G protein-coupled receptor signaling pathway / plasma membrane
Similarity search - Function
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
CHOLESTEROL / (2~{S},5~{R})-hexane-2,5-diol / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Succinate receptor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 Å
AuthorsHaffke, M. / Jaakola, V.-P.
CitationJournal: Nature / Year: 2019
Title: Structural basis of species-selective antagonist binding to the succinate receptor.
Authors: Haffke, M. / Fehlmann, D. / Rummel, G. / Boivineau, J. / Duckely, M. / Gommermann, N. / Cotesta, S. / Sirockin, F. / Freuler, F. / Littlewood-Evans, A. / Kaupmann, K. / Jaakola, V.P.
History
DepositionNov 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Succinate receptor 1
B: Nanobody6
C: Succinate receptor 1
D: Nanobody6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,77723
Polymers110,7404
Non-polymers6,03719
Water5,386299
1
A: Succinate receptor 1
B: Nanobody6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,43312
Polymers55,3702
Non-polymers3,06310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Succinate receptor 1
D: Nanobody6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,34411
Polymers55,3702
Non-polymers2,9759
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.220, 164.000, 63.420
Angle α, β, γ (deg.)90.00, 102.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Antibody , 2 types, 4 molecules ACBD

#1: Protein Succinate receptor 1 / G-protein coupled receptor 91


Mass: 39842.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sucnr1, Gpr91 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6IYF9
#2: Antibody Nanobody6


Mass: 15527.099 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Spodoptera frugiperda (fall armyworm)

-
Non-polymers , 5 types, 318 molecules

#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-H95 / (2~{S},5~{R})-hexane-2,5-diol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 0.1M Na-Citrate 24-30% PEG400 0.05M NaSCN 2.5% 2,5-Hexanediol 1% DMSO
PH range: 4.8-5.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.42→41.55 Å / Num. obs: 198484 / % possible obs: 88.2 % / Redundancy: 17.88 % / Biso Wilson estimate: 44.21 Å2 / Rmerge(I) obs: 0.763 / Net I/σ(I): 2.92
Reflection shellResolution: 1.42→1.46 Å / Redundancy: 1.59 % / Rmerge(I) obs: 2.119 / Mean I/σ(I) obs: 0.32 / % possible all: 20.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XSCALEBUILT 20160617data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
XDSBUILT 20160617data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNV

4xnv


Resolution: 2.12→41.55 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.331 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1950 4.73 %RANDOM
Rwork0.178 ---
obs0.18 41256 61 %-
Displacement parametersBiso mean: 56.4 Å2
Baniso -1Baniso -2Baniso -3
1-11.4567 Å20 Å22.4984 Å2
2---10.1644 Å20 Å2
3----1.2923 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.12→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6643 0 374 299 7316
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017186HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089677HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2506SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1133HARMONIC5
X-RAY DIFFRACTIONt_it7186HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion19.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion907SEMIHARMONIC5
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_contact8266SEMIHARMONIC4
LS refinement shellResolution: 2.12→2.27 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2466 -4.72 %
Rwork0.2309 787 -
all0.2316 826 -
obs--6.86 %
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)
11.20010.87910.12613.04820.59491.4525-0.0057-0.06550.0260.11220.0035-0.10650.08850.0140.0023-0.07820.01260.0226-0.226-0.0078-0.125776.271210.070830.8709
22.1869-0.66670.40287.84713.52643.8511-0.13650.17640.1376-0.48690.0865-0.2175-0.4940.13180.04990.0834-0.11960.0069-0.34550.0701-0.118587.288749.590634.9085
30.91070.36830.16014.8875-0.03123.043-0.04190.02150.1142-0.35920.1250.2289-0.5902-0.1688-0.08320.01340.00070.0882-0.32120.0146-0.251570.3636.2272-2.1961
43.3629-0.59071.263210.3437-1.61514.76780.12990.237-0.4591-0.39320.23440.76491.022-0.4381-0.36440.2545-0.1837-0.088-0.3994-0.075-0.190165.3738-33.5554-1.2745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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