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- PDB-2ipu: PFA1 Fab fragment complexed with Abeta 1-8 peptide -

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Basic information

Entry
Database: PDB / ID: 2ipu
TitlePFA1 Fab fragment complexed with Abeta 1-8 peptide
Components
  • (IgG2a Fab fragment ...) x 2
  • abeta 1-8 peptide
KeywordsIMMUNE SYSTEM / wwddd / cdr / abeta
Function / homology
Function and homology information


regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / positive regulation of amyloid fibril formation / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / cholesterol metabolic process / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / neuron projection maintenance / positive regulation of glycolytic process / extracellular matrix organization / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / learning / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / Post-translational protein phosphorylation / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / TAK1-dependent IKK and NF-kappa-B activation / neuromuscular junction / visual learning / serine-type endopeptidase inhibitor activity / recycling endosome / cognition / positive regulation of inflammatory response / positive regulation of interleukin-6 production / neuron cellular homeostasis / Golgi lumen / endocytosis / positive regulation of non-canonical NF-kappaB signal transduction / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cellular response to amyloid-beta / positive regulation of DNA-binding transcription factor activity / G2/M transition of mitotic cell cycle / cell-cell junction / synaptic vesicle / positive regulation of tumor necrosis factor production / regulation of translation
Similarity search - Function
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 ...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. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / 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 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETAMIDE / If kappa light chain / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGardberg, A.S. / Dealwis, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular basis for passive immunotherapy of Alzheimer's disease
Authors: Gardberg, A.S. / Dice, L.T. / Ou, S. / Rich, R.L. / Helmbrecht, E. / Ko, J. / Wetzel, R. / Myszka, D.G. / Patterson, P.H. / Dealwis, C.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Presently, there is no aminoacid sequence database reference available for the two ...SEQUENCE Presently, there is no aminoacid sequence database reference available for the two proteins IGG2A FAB fragment heavy chain and IGG2A FAB fragment light chain kappa

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IgG2a Fab fragment Heavy Chain
H: IgG2a Fab fragment Light Chain Kappa
K: IgG2a Fab fragment Heavy Chain
G: IgG2a Fab fragment Light Chain Kappa
P: abeta 1-8 peptide
Q: abeta 1-8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,17015
Polymers98,4406
Non-polymers7309
Water2,126118
1
L: IgG2a Fab fragment Heavy Chain
H: IgG2a Fab fragment Light Chain Kappa
Q: abeta 1-8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6148
Polymers49,2203
Non-polymers3945
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: IgG2a Fab fragment Heavy Chain
G: IgG2a Fab fragment Light Chain Kappa
P: abeta 1-8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5557
Polymers49,2203
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.070, 70.335, 74.197
Angle α, β, γ (deg.)72.32, 86.08, 86.02
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a heterodimer with abeta peptide at the interface.

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Components

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Protein/peptide , 1 types, 2 molecules PQ

#3: Protein/peptide abeta 1-8 peptide


Mass: 977.975 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (humans)
References: UniProt: P05067*PLUS

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Antibody , 2 types, 4 molecules LKHG

#1: Antibody IgG2a Fab fragment Heavy Chain


Mass: 24146.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: A2NHM3*PLUS
#2: Antibody IgG2a Fab fragment Light Chain Kappa


Mass: 24095.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c

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Non-polymers , 3 types, 127 molecules

#4: Chemical ChemComp-ACM / ACETAMIDE / Acetamide


Mass: 59.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 20, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→23.53 Å / Num. obs: 90408 / % possible obs: 90.7 % / Redundancy: 3.1 % / Rsym value: 0.055
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.467 / % possible all: 66.3

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IQ9

2iq9


Resolution: 1.65→23.53 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.106 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4515 5 %RANDOM
Rwork0.182 ---
obs0.184 90407 90.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.361 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.01 Å20.2 Å2
2---0.01 Å2-0.59 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.65→23.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6846 0 48 118 7012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227230
X-RAY DIFFRACTIONr_bond_other_d0.0010.024840
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9559898
X-RAY DIFFRACTIONr_angle_other_deg0.876311887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3323.818275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.138151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.751533
X-RAY DIFFRACTIONr_chiral_restr0.0870.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021445
X-RAY DIFFRACTIONr_nbd_refined0.1880.21106
X-RAY DIFFRACTIONr_nbd_other0.20.24918
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23353
X-RAY DIFFRACTIONr_nbtor_other0.0850.23916
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2533
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.274
X-RAY DIFFRACTIONr_mcbond_it1.0451.55871
X-RAY DIFFRACTIONr_mcbond_other0.1921.51835
X-RAY DIFFRACTIONr_mcangle_it1.23427438
X-RAY DIFFRACTIONr_scbond_it1.95433178
X-RAY DIFFRACTIONr_scangle_it2.6134.52426
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 206 -
Rwork0.325 4083 -
obs-4289 58.59 %

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