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- PDB-4ong: Fab fragment of 3D6 in complex with amyloid beta 1-40 -

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Basic information

Entry
Database: PDB / ID: 4ong
TitleFab fragment of 3D6 in complex with amyloid beta 1-40
Components
  • (3D6 FAB ANTIBODY ...) x 2
  • Amyloid beta A4 protein
KeywordsIMMUNE SYSTEM / ANTIBODY / AMYLOID BETA PEPTIDE
Function / homology
Function and homology information


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 / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway ...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 / 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 / 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 / Lysosome Vesicle Biogenesis / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / positive regulation of protein metabolic process / dendrite development / TRAF6 mediated NF-kB activation / modulation of excitatory postsynaptic potential / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / main axon / transition metal ion binding / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / ECM proteoglycans / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / cellular response to manganese ion / clathrin-coated pit / Notch signaling pathway / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / axonogenesis / response to interleukin-1 / positive regulation of mitotic cell cycle / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / adult locomotory behavior / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / endosome lumen / dendritic shaft / TAK1-dependent IKK and NF-kappa-B activation / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / microglial cell activation / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / cellular response to nerve growth factor stimulus / visual learning / recycling endosome / response to lead ion / positive regulation of interleukin-6 production / Golgi lumen / cognition / 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 / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of gene expression / regulation of translation / early endosome membrane / G alpha (i) signalling events / perikaryon / G alpha (q) signalling events / dendritic spine
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. / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFeinberg, H. / Saldanha, J.W. / Diep, L. / Goel, A. / Widom, A. / Veldman, G.M. / Weis, W.I. / Schenk, D. / Basi, G.S.
CitationJournal: Alzheimers Res Ther / Year: 2014
Title: Crystal structure reveals conservation of amyloid-beta conformation recognized by 3D6 following humanization to bapineuzumab.
Authors: Feinberg, H. / Saldanha, J.W. / Diep, L. / Goel, A. / Widom, A. / Veldman, G.M. / Weis, W.I. / Schenk, D. / Basi, G.S.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 3, 2024Group: 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_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 3D6 FAB ANTIBODY HEAVY CHAIN
L: 3D6 FAB ANTIBODY LIGHT CHAIN
P: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,79044
Polymers52,4273
Non-polymers2,36341
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-826 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.04, 84.94, 175.69
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11H-301-

ZN

21L-303-

ZN

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide Amyloid beta A4 protein


Mass: 4335.852 Da / Num. of mol.: 1 / Fragment: unp residues 672-711 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067

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Antibody , 2 types, 2 molecules HL

#1: Antibody 3D6 FAB ANTIBODY HEAVY CHAIN


Mass: 23827.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 3D6 FAB ANTIBODY LIGHT CHAIN


Mass: 24263.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 288 molecules

#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.5 M NaCl, 0.1 Imidazole pH 8.0, 0.2 ZnAc2., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: MAR / Detector: CCD / Date: Mar 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→87.845 Å / Num. obs: 31474 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 22.99 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 19.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.265.90.1893.81342422720.189100
2.26-2.325.90.1784.11310222240.178100
2.32-2.395.90.1544.81276121760.154100
2.39-2.465.90.1415.11235620930.141100
2.46-2.545.90.1285.81216720690.128100
2.54-2.635.90.116.71153719560.11100
2.63-2.735.90.0967.51132919220.096100
2.73-2.845.80.0868.41098018780.086100
2.84-2.975.90.0749.41027617330.074100
2.97-3.115.80.06410.61003917230.064100
3.11-3.285.90.05412.3949216150.054100
3.28-3.485.90.04613.9900015380.046100
3.48-3.725.80.04215.2844014550.042100
3.72-4.025.80.04612.9792713760.046100
4.02-4.45.80.04214.7726012480.042100
4.4-4.925.70.03716.3656011420.037100
4.92-5.685.60.03617.2588610460.036100
5.68-6.965.60.03417.948798700.034100
6.96-9.845.40.02919.938257080.029100
9.84-87.8454.80.03115.720494300.03199.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-IceIcedata collection
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D6 FAB ANTIBODY

Resolution: 2.2→76.474 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8636 / SU ML: 0.2 / σ(F): 0 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1584 5.04 %
Rwork0.177 --
obs0.18 31429 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.91 Å2 / Biso mean: 29.38 Å2 / Biso min: 6.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→76.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 53 247 3601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083507
X-RAY DIFFRACTIONf_angle_d1.1814642
X-RAY DIFFRACTIONf_chiral_restr0.08523
X-RAY DIFFRACTIONf_plane_restr0.005587
X-RAY DIFFRACTIONf_dihedral_angle_d12.4281233
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.2710.22731260.164826622788
2.271-2.35220.27221320.170226972829
2.3522-2.44640.24731610.183626202781
2.4464-2.55770.25611500.18526582808
2.5577-2.69260.26231280.194127182846
2.6926-2.86130.2491390.200927112850
2.8613-3.08220.24071260.193826892815
3.0822-3.39240.24231640.180826882852
3.3924-3.88330.20251650.162627082873
3.8833-4.89240.1841440.144827712915
4.8924-76.51990.22431490.196729233072
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)
15.58351.03840.59911.69780.08732.3414-0.0826-0.0722-0.029-0.00770.0589-0.1029-0.07480.13040.02610.1390.0140.01940.15730.01140.115523.035612.1142116.6332
22.17840.7769-2.42562.7449-1.79376.16150.06870.1470.0611-0.06670.04850.0229-0.0259-0.1454-0.09070.12770.0064-0.01750.0716-0.01330.165816.35611.12186.6878
31.89910.14210.67362.5239-1.04113.601-0.0823-0.02330.23260.1947-0.0147-0.1972-0.58220.41010.07560.3607-0.0622-0.0560.1771-0.00580.217428.324232.9934112.4508
44.21622.98531.76582.3621.49581.9648-0.00510.0270.03180.08080.01520.0593-0.1528-0.09-0.02240.18920.0292-0.00420.10780.03710.20727.45924.500982.612
53.4494-1.752-2.5137.1685.02564.12550.0531-0.25090.19970.33060.1037-0.4711-0.36040.1537-0.11750.18120.0214-0.03160.0833-0.02440.213229.797521.4216126.5929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 119 )H0
2X-RAY DIFFRACTION2chain 'H' and (resid 120 through 219 )H0
3X-RAY DIFFRACTION3chain 'L' and (resid 1 through 111 )L0
4X-RAY DIFFRACTION4chain 'L' and (resid 112 through 216 )L0
5X-RAY DIFFRACTION5chain 'P' and (resid 1 through 5 )P0

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