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- PDB-5csz: CRYSTAL STRUCTURE OF GANTENERUMAB FAB FRAGMENT IN COMPLEX WITH AB... -

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Basic information

Entry
Database: PDB / ID: 5csz
TitleCRYSTAL STRUCTURE OF GANTENERUMAB FAB FRAGMENT IN COMPLEX WITH ABETA 1-11
Components
  • (GANTENERUMAB FAB FRAGMENT ...) x 2
  • Amyloid beta A4 protein
KeywordsIMMUNE SYSTEM / ANTIBODY / ALZHEIMER / ABETA / GANTENERUMAB / GANT_ABETA_1_11 09-A
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 / axo-dendritic transport / regulation of Wnt signaling pathway / hippocampal neuron apoptotic process ...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 / hippocampal neuron apoptotic process / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of synapse structure or activity / 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 / astrocyte projection / Lysosome Vesicle Biogenesis / 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 / negative regulation of long-term synaptic potentiation / signaling receptor activator activity / Advanced glycosylation endproduct receptor signaling / transition metal ion binding / main axon / The NLRP3 inflammasome / modulation of excitatory postsynaptic potential / regulation of multicellular organism growth / intracellular copper ion homeostasis / ECM proteoglycans / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / response to insulin-like growth factor stimulus / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / Notch signaling pathway / cellular response to manganese ion / swimming behavior / clathrin-coated pit / extracellular matrix organization / neuron projection maintenance / astrocyte activation / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / ionotropic glutamate receptor signaling pathway / Mitochondrial protein degradation / response to interleukin-1 / axonogenesis / protein serine/threonine kinase binding / platelet alpha granule lumen / regulation of neuron apoptotic process / cellular response to copper ion / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / dendritic shaft / trans-Golgi network membrane / endosome lumen / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / adult locomotory behavior / learning / Post-translational protein phosphorylation / locomotory behavior / serine-type endopeptidase inhibitor activity / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nerve growth factor stimulus / TAK1-dependent IKK and NF-kappa-B activation / recycling endosome / synapse organization / regulation of long-term neuronal synaptic plasticity / visual learning / positive regulation of JNK cascade / response to lead ion / Golgi lumen / positive regulation of interleukin-6 production / 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 / heparin binding / regulation of translation / regulation of gene expression
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
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsBenz, J. / Burger, D. / Loetscher, H.R. / Bohrmann, B.
CitationJournal: J. Alzheimers Dis. / Year: 2012
Title: Gantenerumab: a novel human anti-Abeta antibody demonstrates sustained cerebral amyloid-Beta binding and elicits cell-mediated removal of human amyloid-Beta.
Authors: Bohrmann, B. / Baumann, K. / Benz, J. / Gerber, F. / Huber, W. / Knoflach, F. / Messer, J. / Oroszlan, K. / Rauchenberger, R. / Richter, W.F. / Rothe, C. / Urban, M. / Bardroff, M. / Winter, ...Authors: Bohrmann, B. / Baumann, K. / Benz, J. / Gerber, F. / Huber, W. / Knoflach, F. / Messer, J. / Oroszlan, K. / Rauchenberger, R. / Richter, W.F. / Rothe, C. / Urban, M. / Bardroff, M. / Winter, M. / Nordstedt, C. / Loetscher, H.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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
H: GANTENERUMAB FAB FRAGMENT HEAVY CHAIN
L: GANTENERUMAB FAB FRAGMENT LIGHT CHAIN
A: GANTENERUMAB FAB FRAGMENT HEAVY CHAIN
B: GANTENERUMAB FAB FRAGMENT LIGHT CHAIN
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,42110
Polymers97,7876
Non-polymers6354
Water13,367742
1
H: GANTENERUMAB FAB FRAGMENT HEAVY CHAIN
L: GANTENERUMAB FAB FRAGMENT LIGHT CHAIN
D: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2115
Polymers48,8933
Non-polymers3172
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-41 kcal/mol
Surface area18880 Å2
MethodPISA
2
A: GANTENERUMAB FAB FRAGMENT HEAVY CHAIN
B: GANTENERUMAB FAB FRAGMENT LIGHT CHAIN
E: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2115
Polymers48,8933
Non-polymers3172
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-42 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.137, 66.242, 105.156
Angle α, β, γ (deg.)90.00, 99.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HALB

#1: Antibody GANTENERUMAB FAB FRAGMENT HEAVY CHAIN


Mass: 24206.119 Da / Num. of mol.: 2 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody GANTENERUMAB FAB FRAGMENT LIGHT CHAIN


Mass: 23359.998 Da / Num. of mol.: 2 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)

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Protein/peptide / Sugars , 2 types, 4 molecules DE

#3: Protein/peptide Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Cerebral vascular amyloid peptide / CVAP / ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 1327.314 Da / Num. of mol.: 2 / Fragment: UNP residues 672-682 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 744 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / 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

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25 % PEG 3350, 0.1M Bis-Tris 6.5, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.8→45.64 Å / Num. obs: 89468 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rsym value: 0.076 / Net I/σ(I): 5.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0062refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.8→45.64 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.918 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23005 4487 5 %RANDOM
Rwork0.19643 ---
obs0.19814 84962 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.464 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.12 Å2
2--0.06 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6622 0 38 742 7402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226814
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9629266
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0723.759266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.848151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8671534
X-RAY DIFFRACTIONr_chiral_restr0.080.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215118
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 316 -
Rwork0.286 6210 -
obs--99.35 %

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