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- PDB-1ca0: BOVINE CHYMOTRYPSIN COMPLEXED TO APPI -

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Basic information

Entry
Database: PDB / ID: 1ca0
TitleBOVINE CHYMOTRYPSIN COMPLEXED TO APPI
Components
  • (BOVINE CHYMOTRYPSIN) x 3
  • PROTEASE INHIBITOR DOMAIN OF ALZHEIMER'S AMYLOID BETA-PROTEIN PRECURSOR
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / SERINE PROTEASE / INHIBITOR / PROTEASE-SUBSTRATE INTERACTIONS / COMPLEX (SERINE PROTEASE-INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


chymotrypsin / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway ...chymotrypsin / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Lysosome Vesicle Biogenesis / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / main axon / transition metal ion binding / intracellular copper ion homeostasis / regulation of multicellular organism growth / serpin family protein binding / ECM proteoglycans / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / serine protease inhibitor complex / positive regulation of chemokine production / digestion / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / axonogenesis / protein serine/threonine kinase binding / response to interleukin-1 / platelet alpha granule lumen / cellular response to copper ion / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / endosome lumen / positive regulation of interleukin-1 beta production / dendritic shaft / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / adult locomotory behavior / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / serine-type endopeptidase inhibitor activity / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / regulation of long-term neuronal synaptic plasticity / cellular response to nerve growth factor stimulus / recycling endosome / synapse organization / visual learning / response to lead ion / positive regulation of interleukin-6 production / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis / cellular response to amyloid-beta / neuron projection development / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of translation / regulation of gene expression / early endosome membrane
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / 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 / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / PH-like domain superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chymotrypsinogen A / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsScheidig, A.J. / Kossiakoff, A.A.
Citation
Journal: Protein Sci. / Year: 1997
Title: Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): ...Title: Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities.
Authors: Scheidig, A.J. / Hynes, T.R. / Pelletier, L.A. / Wells, J.A. / Kossiakoff, A.A.
#1: Journal: Biochemistry / Year: 1990
Title: X-Ray Crystal Structure of the Protease Inhibitor Domain of Alzheimer'S Amyloid Beta-Protein Precursor
Authors: Hynes, T.R. / Randal, M. / Kennedy, L.A. / Eigenbrot, C. / Kossiakoff, A.A.
History
DepositionJan 23, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BOVINE CHYMOTRYPSIN
B: BOVINE CHYMOTRYPSIN
C: BOVINE CHYMOTRYPSIN
D: PROTEASE INHIBITOR DOMAIN OF ALZHEIMER'S AMYLOID BETA-PROTEIN PRECURSOR
F: BOVINE CHYMOTRYPSIN
G: BOVINE CHYMOTRYPSIN
H: BOVINE CHYMOTRYPSIN
I: PROTEASE INHIBITOR DOMAIN OF ALZHEIMER'S AMYLOID BETA-PROTEIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)62,5368
Polymers62,5368
Non-polymers00
Water4,720262
1
A: BOVINE CHYMOTRYPSIN
B: BOVINE CHYMOTRYPSIN
C: BOVINE CHYMOTRYPSIN
D: PROTEASE INHIBITOR DOMAIN OF ALZHEIMER'S AMYLOID BETA-PROTEIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)31,2684
Polymers31,2684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-70 kcal/mol
Surface area12070 Å2
MethodPISA
2
F: BOVINE CHYMOTRYPSIN
G: BOVINE CHYMOTRYPSIN
H: BOVINE CHYMOTRYPSIN
I: PROTEASE INHIBITOR DOMAIN OF ALZHEIMER'S AMYLOID BETA-PROTEIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)31,2684
Polymers31,2684
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-69 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.522, 181.488, 46.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.782832, 0.018759, 0.62195), (-0.04656, 0.994977, -0.088614), (-0.620489, -0.098327, -0.778027)
Vector: 29.6121, -14.3147, 74.2506)

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Components

#1: Protein/peptide BOVINE CHYMOTRYPSIN


Mass: 1253.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein BOVINE CHYMOTRYPSIN


Mass: 13934.556 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: A4 / Organ: PANCREATIC / Plasmid: PA4G32R / Gene (production host): A4 / Production host: Escherichia coli (E. coli) / Strain (production host): 27C7 / References: UniProt: P00766, chymotrypsin
#3: Protein BOVINE CHYMOTRYPSIN


Mass: 10074.495 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: A4 / Organ: PANCREATIC / Plasmid: PA4G32R / Gene (production host): A4 / Production host: Escherichia coli (E. coli) / Strain (production host): 27C7 / References: UniProt: P00766, chymotrypsin
#4: Protein PROTEASE INHIBITOR DOMAIN OF ALZHEIMER'S AMYLOID BETA-PROTEIN PRECURSOR / APPI


Mass: 6005.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: A4 / Organ: PANCREATIC / Plasmid: PA4G32R / Gene (production host): A4 / Production host: Escherichia coli (E. coli) / Strain (production host): 27C7 / References: UniProt: P05067
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.09 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-12.5 %(w/v)PEG60001reservoir
2100 mMsodium citrate1reservoir
35 %(v/v)dimethylacetamide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1994 / Details: MIRROR
RadiationMonochromator: MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. obs: 33088 / % possible obs: 81.1 % / Redundancy: 3.05 % / Biso Wilson estimate: 37.8 Å2 / Rsym value: 0.0298 / Net I/σ(I): 39.87
Reflection
*PLUS
Rmerge(I) obs: 0.03

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.1→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: YES / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.323 -8.6 %RANDOM
Rwork0.215 ---
obs0.215 30005 85 %-
Displacement parametersBiso mean: 39.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.29 Å
Luzzati d res low-8 Å
Luzzati sigma a0.34 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 0 262 4608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.402
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.245
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.427 247 7.2 %
Rwork0.391 2219 -
obs--72.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.21
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.245

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