[English] 日本語
Yorodumi
- PDB-3u8d: Functionally selective inhibition of Group IIA phospholipase A2 r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u8d
TitleFunctionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism
ComponentsPhospholipase A2, membrane associated
KeywordsHYDROLASE / secreted phospholipase A2 / Phospholipase A2 activity
Function / homology
Function and homology information


regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA ...regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / phosphatidylcholine metabolic process / phospholipase A2 activity / positive regulation of macrophage derived foam cell differentiation / low-density lipoprotein particle remodeling / calcium-dependent phospholipase A2 activity / phospholipase A2 / Antimicrobial peptides / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / secretory granule / phospholipid binding / positive regulation of inflammatory response / killing of cells of another organism / mitochondrial outer membrane / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-U8D / Phospholipase A2, membrane associated
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å
AuthorsLee, L.K. / Bryant, K.J. / Bouveret, R. / Lei, P.-W. / Duff, A.P. / Harrop, S.J. / Huang, E.P. / Harvey, R.P. / Gelb, M.H. / Gray, P.P. ...Lee, L.K. / Bryant, K.J. / Bouveret, R. / Lei, P.-W. / Duff, A.P. / Harrop, S.J. / Huang, E.P. / Harvey, R.P. / Gelb, M.H. / Gray, P.P. / Curmi, P.M. / Cunningham, A.M. / Church, W.B. / Scott, K.F.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Selective Inhibition of Human Group IIA-secreted Phospholipase A2 (hGIIA) Signaling Reveals Arachidonic Acid Metabolism Is Associated with Colocalization of hGIIA to Vimentin in Rheumatoid Synoviocytes.
Authors: Lee, L.K. / Bryant, K.J. / Bouveret, R. / Lei, P.W. / Duff, A.P. / Harrop, S.J. / Huang, E.P. / Harvey, R.P. / Gelb, M.H. / Gray, P.P. / Curmi, P.M. / Cunningham, A.M. / Church, W.B. / Scott, K.F.
History
DepositionOct 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phospholipase A2, membrane associated
B: Phospholipase A2, membrane associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,05312
Polymers27,8902
Non-polymers1,16310
Water6,035335
1
A: Phospholipase A2, membrane associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5276
Polymers13,9451
Non-polymers5815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phospholipase A2, membrane associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5276
Polymers13,9451
Non-polymers5815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.422, 74.422, 93.674
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-205-

CL

21A-351-

HOH

31A-417-

HOH

41A-458-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 125
2115B1 - 125

-
Components

#1: Protein Phospholipase A2, membrane associated / GIIC sPLA2 / Group IIA phospholipase A2 / Non-pancreatic secretory phospholipase A2 / NPS-PLA2 / ...GIIC sPLA2 / Group IIA phospholipase A2 / Non-pancreatic secretory phospholipase A2 / NPS-PLA2 / Phosphatidylcholine 2-acylhydrolase 2A


Mass: 13945.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G2A, PLA2B, PLA2L, RASF-A / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14555, phospholipase A2
#2: Chemical ChemComp-U8D / (3-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-ethyl-1H-indol-5-yl]oxy}propyl)phosphonic acid


Mass: 430.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N2O5P
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Tris-HCl pH 7.4, 10 mM CaCl2, 0.5 mM beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2006
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11K, H, -L20.5
ReflectionResolution: 1.801→37.178 Å / Num. obs: 28140 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.5

-
Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.805→19.82 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.81 / σ(F): 1.34 / Phase error: 19.41 / Stereochemistry target values: TWIN_LSQ_F / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1893 2101 7.5 %
Rwork0.1214 --
obs0.1264 27471 99.64 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.77 Å2 / ksol: 0.398 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9304 Å2-0 Å2-0 Å2
2--2.9304 Å20 Å2
3----5.8608 Å2
Refinement stepCycle: LAST / Resolution: 1.805→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 68 335 2335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162115
X-RAY DIFFRACTIONf_angle_d1.2092859
X-RAY DIFFRACTIONf_dihedral_angle_d21.494805
X-RAY DIFFRACTIONf_chiral_restr0.091278
X-RAY DIFFRACTIONf_plane_restr0.004356
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
724medium positional0.270.5
968loose positional0.475
724medium thermal0.632
968loose thermal0.7710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.805-1.84720.30311370.18211662X-RAY DIFFRACTION90
1.8472-1.89340.23751360.16661711X-RAY DIFFRACTION92
1.8934-1.94450.22831380.15981694X-RAY DIFFRACTION92
1.9445-2.00160.25861400.15151712X-RAY DIFFRACTION92
2.0016-2.06610.21971430.14021715X-RAY DIFFRACTION92
2.0661-2.13980.19841380.1351704X-RAY DIFFRACTION93
2.1398-2.22530.18361410.13081722X-RAY DIFFRACTION92
2.2253-2.32640.1931390.13391715X-RAY DIFFRACTION93
2.3264-2.44870.1621380.12751711X-RAY DIFFRACTION93
2.4487-2.60160.18981420.12151723X-RAY DIFFRACTION92
2.6016-2.80160.22031350.11921729X-RAY DIFFRACTION93
2.8016-3.0820.20231380.12351743X-RAY DIFFRACTION93
3.082-3.52440.17221390.1011751X-RAY DIFFRACTION92
3.5244-4.42710.13041440.08441769X-RAY DIFFRACTION92
4.4271-16.88320.16131480.11451833X-RAY DIFFRACTION92

+
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://pdbjlvh1.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