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- PDB-6pxr: Anti-TAU BIIB092 FAB with TAU peptide -

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Basic information

Entry
Database: PDB / ID: 6pxr
TitleAnti-TAU BIIB092 FAB with TAU peptide
Components
  • Microtubule-associated protein tau
  • gosuranemab Fab, heavy chain
  • gosuranemab Fab, light chain
KeywordsIMMUNE SYSTEM / TAU / antibody / BIIB092 / gosuranemab tau complex
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / : / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle assembly / positive regulation of protein localization to synapse / neurofibrillary tangle / microtubule lateral binding / axonal transport / main axon ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / : / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle assembly / positive regulation of protein localization to synapse / neurofibrillary tangle / microtubule lateral binding / axonal transport / main axon / phosphatidylinositol bisphosphate binding / tubulin complex / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / internal protein amino acid acetylation / regulation of chromosome organization / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / intracellular distribution of mitochondria / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / negative regulation of mitochondrial membrane potential / apolipoprotein binding / : / glial cell projection / protein polymerization / negative regulation of mitochondrial fission / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cytoplasmic microtubule organization / Activation of AMPK downstream of NMDARs / synapse assembly / positive regulation of protein localization / axon cytoplasm / regulation of calcium-mediated signaling / supramolecular fiber organization / stress granule assembly / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / positive regulation of microtubule polymerization / phosphatidylinositol binding / nuclear periphery / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / cellular response to reactive oxygen species / astrocyte activation / Hsp90 protein binding / microglial cell activation / synapse organization / cellular response to nerve growth factor stimulus / response to lead ion / PKR-mediated signaling / protein homooligomerization / regulation of synaptic plasticity / SH3 domain binding / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / microtubule cytoskeleton / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / actin binding / cell body / cellular response to heat / growth cone / double-stranded DNA binding / microtubule binding / protein-macromolecule adaptor activity / sequence-specific DNA binding / microtubule / amyloid fibril formation / dendritic spine / learning or memory / neuron projection / nuclear speck / membrane raft / axon / negative regulation of gene expression / neuronal cell body / dendrite / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding
Similarity search - Function
Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
If kappa light chain / Microtubule-associated protein tau
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.556 Å
AuthorsArndt, J.W. / Quan, C.
CitationJournal: Neurobiol.Dis. / Year: 2020
Title: Characterization of tau binding by gosuranemab.
Authors: Sopko, R. / Golonzhka, O. / Arndt, J. / Quan, C. / Czerkowicz, J. / Cameron, A. / Smith, B. / Murugesan, Y. / Gibbons, G. / Kim, S.J. / Trojanowski, J.Q. / Lee, V.M.Y. / Brunden, K.R. / ...Authors: Sopko, R. / Golonzhka, O. / Arndt, J. / Quan, C. / Czerkowicz, J. / Cameron, A. / Smith, B. / Murugesan, Y. / Gibbons, G. / Kim, S.J. / Trojanowski, J.Q. / Lee, V.M.Y. / Brunden, K.R. / Graham, D.L. / Weinreb, P.H. / Hering, H.
History
DepositionJul 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _struct_keywords.text
Revision 1.2Nov 20, 2024Group: 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
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
L: gosuranemab Fab, light chain
H: gosuranemab Fab, heavy chain
A: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)48,7723
Polymers48,7723
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-27 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.745, 48.952, 58.653
Angle α, β, γ (deg.)85.250, 83.120, 70.720
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody gosuranemab Fab, light chain


Mass: 24110.754 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) / References: UniProt: A2NHM3
#2: Antibody gosuranemab Fab, heavy chain


Mass: 23908.895 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)
#3: Protein/peptide Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 752.772 Da / Num. of mol.: 1 / Fragment: UNP residues 15-22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPT, MAPTL, MTBT1, TAU / Production host: Homo sapiens (human) / References: UniProt: P10636
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl, pH 8.5, 20% w/v PEG2000 MME, 200 mM trimethylamine N-oxide, 100 mM non-detergent sulfobetaine 201

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 28, 2018
RadiationMonochromator: double crystal diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.556→24.74 Å / Num. obs: 61209 / % possible obs: 95.8 % / Redundancy: 2 % / Net I/σ(I): 7.1
Reflection shellResolution: 1.556→1.61 Å / Num. unique obs: 6045

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.556→24.737 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 29.13
RfactorNum. reflection% reflection
Rfree0.2683 2979 4.87 %
Rwork0.2278 --
obs0.2298 61204 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66 Å2 / Biso mean: 24.2386 Å2 / Biso min: 10.23 Å2
Refinement stepCycle: final / Resolution: 1.556→24.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 394 3719
Biso mean---32.5 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053429
X-RAY DIFFRACTIONf_angle_d0.8874664
X-RAY DIFFRACTIONf_chiral_restr0.033524
X-RAY DIFFRACTIONf_plane_restr0.005592
X-RAY DIFFRACTIONf_dihedral_angle_d11.5521219
LS refinement shellResolution: 1.5563→1.5818 Å / Rfactor Rfree error: 0 /
Num. reflection% reflection
Rfree142 -
Rwork2762 -
obs-93 %
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)
11.80231.5166-0.40774.8709-1.37970.7322-0.01070.10210.2960.06110.13980.5248-0.1047-0.1137-0.15220.17870.0279-0.02180.2443-0.01110.2113-2.31561.9726-19.7341
24.09161.8875-1.07521.33030.52837.38990.2462-0.2882-0.17650.1889-0.169-0.15150.29720.5537-0.03690.2110.0069-0.00080.1442-0.00080.14027.5578-2.4024-12.3869
32.40320.6195-0.15881.7553-0.16672.5828-0.06230.1964-0.0987-0.0810.03750.12680.18820.01140.03270.1650.009-0.00340.1473-0.0030.14414.0405-5.1632-20.1364
42.71162.6584-1.99752.7839-2.26751.84480.0152-0.21030.1566-0.2161-0.12310.20140.17310.14690.06080.17550.0126-0.00720.1696-0.03280.1602-3.6989-2.5184-10.321
51.8776-0.7597-1.5391.60170.79931.20760.1034-0.10630.0906-0.1363-0.0165-0.0309-0.1232-0.0134-0.09890.13110.0023-0.00030.1598-0.00190.1125-16.8178-2.776712.4595
62.1056-1.2327-2.20311.58411.94123.4910.10230.04950.0108-0.1309-0.07370.0234-0.0654-0.18-0.05870.12510.0044-0.00350.16140.01310.1111-19.019-4.891812.0677
73.43760.3285-1.18670.84-1.13725.7544-0.2013-0.1056-0.27630.2306-0.04340.04890.04640.47760.13110.1547-0.0437-0.05730.14560.00420.070315.42529.34244.0778
81.88830.2385-0.67921.8841-0.18663.66840.0262-0.02520.12580.0860.0199-0.2101-0.11980.3573-0.02790.1563-0.001-0.01260.1475-0.0220.130516.348112.8898-7.4581
91.83020.2141-1.50781.91481.36244.42150.1433-0.03060.10250.18040.05820.0665-0.28290.031-0.14520.20030.0368-0.00180.152-0.00970.11828.860111.95170.3492
100.70310.1517-0.42490.52040.242.65020.1156-0.0775-0.07380.0474-0.08440.067-0.0766-0.05790.00930.08790.0623-0.03990.08560.00610.15841.5267-0.83889.0467
113.68443.11170.5083.73890.35642.65750.0839-0.02430.02010.01850.06270.1136-0.02940.0778-0.14340.07560.0039-0.00210.1532-0.01150.1891-2.5561-7.331815.2332
125.1143.4484-1.0164.3464-0.60022.060.4229-0.5086-0.3620.255-0.25890.14950.4942-0.3584-0.13470.286-0.1121-0.06880.31340.07960.2148-5.5851-12.995924.8673
135.44164.43913.8667.20914.1725.4794-0.17920.66920.0224-0.11430.6925-0.2468-0.08930.8098-0.32120.2111-0.03570.0180.2946-0.04090.202918.01312.0148-21.888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 37 )L1 - 37
2X-RAY DIFFRACTION2chain 'L' and (resid 38 through 53 )L38 - 53
3X-RAY DIFFRACTION3chain 'L' and (resid 54 through 95 )L54 - 95
4X-RAY DIFFRACTION4chain 'L' and (resid 96 through 118 )L96 - 118
5X-RAY DIFFRACTION5chain 'L' and (resid 119 through 168 )L119 - 168
6X-RAY DIFFRACTION6chain 'L' and (resid 169 through 218 )L169 - 218
7X-RAY DIFFRACTION7chain 'H' and (resid 2 through 17 )H2 - 17
8X-RAY DIFFRACTION8chain 'H' and (resid 18 through 83 )H18 - 83
9X-RAY DIFFRACTION9chain 'H' and (resid 84 through 98 )H84 - 98
10X-RAY DIFFRACTION10chain 'H' and (resid 99 through 149 )H99 - 149
11X-RAY DIFFRACTION11chain 'H' and (resid 150 through 188 )H150 - 188
12X-RAY DIFFRACTION12chain 'H' and (resid 189 through 218 )H189 - 218
13X-RAY DIFFRACTION13chain 'A' and (resid 15 through 22 )A15 - 22

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