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Basic information

Entry
Database: PDB / ID: 3gci
TitleCrystal Structure of the Complex Formed Between a New Isoform of Phospholipase A2 with C-terminal Amyloid Beta Heptapeptide at 2 A Resolution
Components
  • Heptapeptide from Amyloid beta A4 protein
  • Phospholipase A2 isoform 3
KeywordsHYDROLASE / PHOSPHOLIPASE A2 / HEPTAPEPTIDE / AMYLOID BETA / Lipid degradation / Metal-binding / Secreted
Function / homology
Function and homology information


amyloid-beta complex / microglia development / negative regulation of presynapse assembly / phospholipase A2 / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / calcium-dependent phospholipase A2 activity / regulation of synapse structure or activity ...amyloid-beta complex / microglia development / negative regulation of presynapse assembly / phospholipase A2 / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / calcium-dependent phospholipase A2 activity / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition / astrocyte activation involved in immune response / smooth endoplasmic reticulum calcium ion homeostasis / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / arachidonate secretion / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / suckling behavior / COPII-coated ER to Golgi transport vesicle / positive regulation of protein metabolic process / dendrite development / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / neuromuscular process controlling balance / transition metal ion binding / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / forebrain development / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / lipid catabolic process / positive regulation of chemokine production / phospholipid metabolic process / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / axonogenesis / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / cholesterol metabolic process / response to interleukin-1 / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / platelet alpha granule lumen / positive regulation of glycolytic process / adult locomotory behavior / dendritic shaft / positive regulation of long-term synaptic potentiation / central nervous system development / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / endosome lumen / learning / locomotory behavior / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / microglial cell activation / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / synapse organization / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / neuromuscular junction / visual learning / recycling endosome / phospholipid binding / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / positive regulation of fibroblast proliferation / cellular response to amyloid-beta
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Phospholipase A2 / Phospholipase A2 ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Phospholipase A2 domain superfamily / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Amyloid-beta precursor protein / Acidic phospholipase A2 3
Similarity search - Component
Biological speciesNaja sagittifera (cobra)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsMirza, Z. / Vikram, G. / Singh, N. / Sinha, M. / Bhushan, A. / Sharma, S. / Srinivasan, A. / Kaur, P. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of the Complex Formed Between a New Isoform of Phospholipase A2 with C-terminal Amyloid Beta Heptapeptide at 2 A Resolution
Authors: Mirza, Z. / Vikram, G. / Singh, N. / Sinha, M. / Bhushan, A. / Sharma, S. / Srinivasan, A. / Kaur, P. / Singh, T.P.
History
DepositionFeb 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Derived calculations
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2 isoform 3
P: Heptapeptide from Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7483
Polymers13,7082
Non-polymers401
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-20 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.679, 42.679, 65.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Phospholipase A2 isoform 3 / Phosphatidylcholine 2-acylhydrolase


Mass: 13094.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / References: UniProt: P60045, phospholipase A2
#2: Protein/peptide Heptapeptide from Amyloid beta A4 protein


Mass: 613.747 Da / Num. of mol.: 1 / Fragment: UNP residues 707-713 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. This sequence occurs naturally in humans.
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05067
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN CHAIN A, RESIDUE NUMBER 16 IS SIMPLY SKIPPED. THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND ...IN CHAIN A, RESIDUE NUMBER 16 IS SIMPLY SKIPPED. THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND THESE MUTATIONS ARE PRESENT IN THE DEPOSITED SEQUENCE.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10mM Sodium phosphate, pH 6.0, 1mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 2008 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→20 Å / Num. all: 7596 / Num. obs: 7596 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.115 / Net I/σ(I): 7.8
Reflection shellResolution: 2.04→2.09 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.305 / % possible all: 96.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
MOLREPphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MF4

1mf4


Resolution: 2.04→19.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.618 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.232 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22137 340 4.6 %RANDOM
Rwork0.18436 ---
all0.19 7596 --
obs0.18606 7065 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.418 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.04→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 1 93 1043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022972
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.9351319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8845123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.772548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61115145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.796155
X-RAY DIFFRACTIONr_chiral_restr0.1030.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02761
X-RAY DIFFRACTIONr_nbd_refined0.2030.2429
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.265
X-RAY DIFFRACTIONr_metal_ion_refined0.0130.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.30.217
X-RAY DIFFRACTIONr_mcbond_it0.7321.5636
X-RAY DIFFRACTIONr_mcangle_it1.4082985
X-RAY DIFFRACTIONr_scbond_it1.8783387
X-RAY DIFFRACTIONr_scangle_it2.9444.5334
LS refinement shellResolution: 2.04→2.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 28 -
Rwork0.257 493 -
obs--96.66 %

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