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- PDB-2r0w: PFA2 FAB complexed with Abeta1-8 -

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Basic information

Entry
Database: PDB / ID: 2r0w
TitlePFA2 FAB complexed with Abeta1-8
Components
  • Amyloid beta peptide fragment
  • IgG2a Fab fragment heavy chain, Fd portion
  • IgG2a Fab fragment light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / Alzheimer disease / amyloid
Function / homology
Function and homology information


amyloid-beta complex / microglia development / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway ...amyloid-beta complex / microglia development / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / 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 / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / immunoglobulin complex / 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 / positive regulation of chemokine production / 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 / 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 / cellular response to amyloid-beta / neuron projection development / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / apical part of cell / synaptic vesicle / Platelet degranulation
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, 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 / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / PH-like domain superfamily / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
If kappa light chain / Amyloid-beta precursor protein / Anti-human Fc gamma receptor III 3G8 gamma heavy chain variable region
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.503 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
DepositionAug 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE RESIDUES L GLU 212 AND L YCM 213 HAVE VERY LONG DISTANCE OF C-N BOND, 1.87, AND MAY NOT BE LINKED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IgG2a Fab fragment light chain
H: IgG2a Fab fragment heavy chain, Fd portion
Q: Amyloid beta peptide fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2254
Polymers49,2023
Non-polymers231
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.793, 43.327, 58.456
Angle α, β, γ (deg.)92.510, 94.960, 90.550
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody IgG2a Fab fragment light chain


Mass: 24203.863 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NHM3
#2: Antibody IgG2a Fab fragment heavy chain, Fd portion


Mass: 24020.068 Da / Num. of mol.: 1 / Fragment: Fd portion of heavy chain / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q811U5
#3: Protein/peptide Amyloid beta peptide fragment / Amyloid beta A4 protein / fragment


Mass: 977.975 Da / Num. of mol.: 1 / Fragment: octapeptide / Source method: obtained synthetically / References: UniProt: P05067
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.3
Details: 25% PEG-MME 5000, 0.1 M OAc, pH 5.3, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→42.64 Å / Num. obs: 13814 / % possible obs: 96 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.071 / Χ2: 1.296 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.591.80.47312811.053189.8
2.59-2.691.90.39813881.026194.8
2.69-2.821.90.31213551.036195.8
2.82-2.9620.22813951.104195.9
2.96-3.151.90.1613841.16196.7
3.15-3.3920.10914001.393197
3.39-3.731.90.08713581.892195.4
3.73-4.271.90.05314271.425197.7
4.27-5.381.90.03514321.453198.6
5.38-501.90.03113941.384198.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0007refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.503→42.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 31.49 / SU ML: 0.337 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 695 5 %RANDOM
Rwork0.208 ---
obs0.211 13800 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.705 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.17 Å20.14 Å2
2--0.35 Å20.07 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.503→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 1 63 3481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213502
X-RAY DIFFRACTIONr_bond_other_d0.0020.023062
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9374771
X-RAY DIFFRACTIONr_angle_other_deg0.84337170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96924.088137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40815564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9951515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02687
X-RAY DIFFRACTIONr_nbd_refined0.2080.2677
X-RAY DIFFRACTIONr_nbd_other0.1940.23116
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21673
X-RAY DIFFRACTIONr_nbtor_other0.0910.22129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.25
X-RAY DIFFRACTIONr_mcbond_it0.5481.52207
X-RAY DIFFRACTIONr_mcbond_other0.1091.5897
X-RAY DIFFRACTIONr_mcangle_it1.0123588
X-RAY DIFFRACTIONr_scbond_it1.43631357
X-RAY DIFFRACTIONr_scangle_it2.2584.51183
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 52 -
Rwork0.289 862 -
all-914 -
obs--87.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2593-0.35761.95840.1193-0.43163.9191-0.0115-0.21570.05850.04920.03050.0804-0.0883-0.6713-0.019-0.0374-0.04460.03350.06450.01720.0741-7.36093.43884.33
21.1167-0.41241.34430.8453-1.00114.71770.04550.204-0.04560.0489-0.05310.00460.4190.3820.00760.0371-0.02950.0588-0.0393-0.01540.03037.0519-2.279-4.859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1121 - 118
2X-RAY DIFFRACTION1LA113 - 213119 - 219
3X-RAY DIFFRACTION2HB1 - 1231 - 133
4X-RAY DIFFRACTION2HB124 - 137134 - 147
5X-RAY DIFFRACTION2HB144 - 213154 - 223

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