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- PDB-5vzy: Crystal structure of crenezumab Fab in complex with Abeta -

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Basic information

Entry
Database: PDB / ID: 5vzy
TitleCrystal structure of crenezumab Fab in complex with Abeta
Components
  • Amyloid beta A4 protein
  • Crenezumab Fab heavy chain,Immunoglobulin gamma-1 heavy chain
  • Crenezumab Fab light chain,Immunoblobulin light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin
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 / immunoglobulin complex / 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 / signaling receptor activator activity / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / transition metal ion binding / main axon / 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 / positive regulation of glycolytic process / cellular response to cAMP / 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 / visual learning / cellular response to nerve growth factor stimulus / recycling endosome / positive regulation of interleukin-6 production / response to lead ion / 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
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 / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein / Immunoglobulin gamma-1 heavy chain / Immunoblobulin light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.32 Å
AuthorsUltsch, M. / Wang, W.
CitationJournal: Sci Rep / Year: 2016
Title: Structure of Crenezumab Complex with Abeta Shows Loss of beta-Hairpin.
Authors: Ultsch, M. / Li, B. / Maurer, T. / Mathieu, M. / Adolfsson, O. / Muhs, A. / Pfeifer, A. / Pihlgren, M. / Bainbridge, T.W. / Reichelt, M. / Ernst, J.A. / Eigenbrot, C. / Fuh, G. / Atwal, J.K. ...Authors: Ultsch, M. / Li, B. / Maurer, T. / Mathieu, M. / Adolfsson, O. / Muhs, A. / Pfeifer, A. / Pihlgren, M. / Bainbridge, T.W. / Reichelt, M. / Ernst, J.A. / Eigenbrot, C. / Fuh, G. / Atwal, J.K. / Watts, R.J. / Wang, W.
History
DepositionMay 29, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionAug 9, 2017ID: 5KNA
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Oct 9, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _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: Crenezumab Fab heavy chain,Immunoglobulin gamma-1 heavy chain
L: Crenezumab Fab light chain,Immunoblobulin light chain
A: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)48,8203
Polymers48,8203
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-29 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.300, 67.130, 126.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Crenezumab Fab heavy chain,Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 22997.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P0DOX5
#2: Antibody Crenezumab Fab light chain,Immunoblobulin light chain


Mass: 24064.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q0KKI6
#3: Protein/peptide Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Beta-amyloid ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Beta-amyloid precursor protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 1757.960 Da / Num. of mol.: 1 / Fragment: UNP residues 682-696
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: unidentified (others) / References: UniProt: P05067
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 1.93 Å3/Da / Density % sol: 36.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M Tris hydrochloride pH 8.5, 30% w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.32→46.085 Å / Num. obs: 30793 / % possible obs: 98.8 % / Redundancy: 4.8 % / Net I/σ(I): 6.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.32→46.085 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 25.46
RfactorNum. reflection% reflection
Rfree0.2493 1580 5.13 %
Rwork0.2058 --
obs0.2081 30793 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.32→46.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 0 142 3449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033388
X-RAY DIFFRACTIONf_angle_d0.7254602
X-RAY DIFFRACTIONf_dihedral_angle_d12.9741208
X-RAY DIFFRACTIONf_chiral_restr0.026518
X-RAY DIFFRACTIONf_plane_restr0.004591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3201-2.3950.33931510.30862479X-RAY DIFFRACTION92
2.395-2.48060.38571070.30322683X-RAY DIFFRACTION97
2.4806-2.57990.33631560.27862726X-RAY DIFFRACTION100
2.5799-2.69730.31931670.26032642X-RAY DIFFRACTION99
2.6973-2.83950.26921410.24472718X-RAY DIFFRACTION99
2.8395-3.01740.27841570.23462704X-RAY DIFFRACTION99
3.0174-3.25030.341700.22032672X-RAY DIFFRACTION99
3.2503-3.57730.2161440.19532493X-RAY DIFFRACTION92
3.5773-4.09460.20351050.16942731X-RAY DIFFRACTION99
4.0946-5.15770.15051410.13152700X-RAY DIFFRACTION99
5.1577-46.09420.16611410.14332665X-RAY DIFFRACTION98
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)
10.0088-0.00380.00380.0174-0.01620.01270.03760.03570.0832-0.01630.0199-0.0186-0.0092-0.03710.05510.080.0513-0.0155-0.03190.05270.031221.158940.0613-0.4213
20.06020.02120.00210.01930.00940.01620.03120.04710.00470.0130.0149-0.04550.0080.01320.00340.06240.0095-0.01790.0387-0.00050.096538.201324.4238-2.2348
30.0007-0.0017-0.00320.01160.01280.01560.0130.0588-0.0283-0.0360.0385-0.11490.00980.080.00680.0645-0.0040.0070.1575-0.03050.113122.173320.1659-32.9182
40.03710.00370.0060.03120.01560.03010.07370.1017-0.0080.02010.0362-0.0179-0.0382-0.05750.07030.0682-0.0180.01150.02340.0504-0.01123.160628.0871-7.908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 1:110 )L1 - 110
2X-RAY DIFFRACTION2( CHAIN H AND RESID 1:114 )H1 - 114
3X-RAY DIFFRACTION3( CHAIN H AND RESID 115:214 )H115 - 214
4X-RAY DIFFRACTION4( CHAIN A AND RESID 101:108 ) OR ( CHAIN H AND RESID 301:355 ) OR ( CHAIN L AND RESID 301:379 )A101 - 108
5X-RAY DIFFRACTION4( CHAIN A AND RESID 101:108 ) OR ( CHAIN H AND RESID 301:355 ) OR ( CHAIN L AND RESID 301:379 )H301 - 355
6X-RAY DIFFRACTION4( CHAIN A AND RESID 101:108 ) OR ( CHAIN H AND RESID 301:355 ) OR ( CHAIN L AND RESID 301:379 )L301 - 379

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