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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


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition / regulation of synapse structure or activity / hippocampal neuron apoptotic process / 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 / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / PTB domain binding / positive regulation of amyloid fibril formation / Golgi-associated vesicle / astrocyte projection / Lysosome Vesicle Biogenesis / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / transition metal ion binding / The NLRP3 inflammasome / main axon / intracellular copper ion homeostasis / modulation of excitatory postsynaptic potential / regulation of multicellular organism growth / ECM proteoglycans / immunoglobulin complex / response to insulin-like growth factor stimulus / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / cellular response to manganese ion / positive regulation of chemokine production / Notch signaling pathway / swimming behavior / neuron projection maintenance / extracellular matrix organization / clathrin-coated pit / positive regulation of mitotic cell cycle / axonogenesis / Mitochondrial protein degradation / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / astrocyte activation / platelet alpha granule lumen / response to interleukin-1 / regulation of neuron apoptotic process / cellular response to copper ion / cellular response to cAMP / positive regulation of glycolytic process / endosome lumen / trans-Golgi network membrane / dendritic shaft / positive regulation of interleukin-1 beta production / protein serine/threonine kinase binding / positive regulation of long-term synaptic potentiation / learning / central nervous system development / adult locomotory behavior / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / locomotory behavior / microglial cell activation / cellular response to nerve growth factor stimulus / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / visual learning / recycling endosome / regulation of long-term neuronal synaptic plasticity / Golgi lumen / positive regulation of interleukin-6 production / positive regulation of JNK cascade / response to lead ion / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / endocytosis / neuron projection development / positive regulation of tumor necrosis factor production / positive regulation of inflammatory response / calcium ion transport / Platelet degranulation / regulation of translation / heparin binding
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, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...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, heparin-binding / Amyloid A4 N-terminal heparin-binding / 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, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / 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 / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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


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


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


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

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Details

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: 2.17 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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