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- PDB-5zia: Crystal structure of human anti-tau antibody CBTAU-24.1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5zia
TitleCrystal structure of human anti-tau antibody CBTAU-24.1 in complex with its phosphorylated tau peptide
Components
  • Heavy chain of CBTAU-24.1 antibody
  • Light chain (kappa) of CBTAU-24.1 antibody
  • phosphorylated tau peptide
KeywordsIMMUNE SYSTEM / antibody / tau protein
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 / microtubule lateral binding / axonal transport / tubulin complex / positive regulation of protein localization to synapse / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / tubulin complex / positive regulation of protein localization to synapse / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding / generation of neurons / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / regulation of chromosome organization / central nervous system neuron development / intracellular distribution of mitochondria / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / microtubule polymerization / negative regulation of mitochondrial membrane potential / regulation of microtubule polymerization / dynactin binding / apolipoprotein binding / main axon / protein polymerization / axolemma / glial cell projection / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / neurofibrillary tangle assembly / positive regulation of axon extension / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / synapse assembly / positive regulation of superoxide anion generation / regulation of long-term synaptic depression / positive regulation of protein localization / cellular response to brain-derived neurotrophic factor stimulus / supramolecular fiber organization / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / somatodendritic compartment / positive regulation of microtubule polymerization / axon cytoplasm / astrocyte activation / phosphatidylinositol binding / stress granule assembly / nuclear periphery / regulation of microtubule cytoskeleton organization / protein phosphatase 2A binding / cellular response to reactive oxygen species / Hsp90 protein binding / microglial cell activation / cellular response to nerve growth factor stimulus / protein homooligomerization / synapse organization / regulation of synaptic plasticity / PKR-mediated signaling / response to lead ion / SH3 domain binding / microtubule cytoskeleton organization / memory / cytoplasmic ribonucleoprotein granule / neuron projection development / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / cellular response to heat / microtubule cytoskeleton / growth cone / cell body / actin binding / double-stranded DNA binding / protein-macromolecule adaptor activity / microtubule binding / dendritic spine / sequence-specific DNA binding / amyloid fibril formation / microtubule / learning or memory / neuron projection / regulation of autophagy / membrane raft / axon / negative regulation of gene expression / neuronal cell body / DNA damage response / dendrite / protein kinase binding / enzyme binding / mitochondrion / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus / plasma membrane
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. / : / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsZhang, H. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)P41GM103393 United States
CitationJournal: Structure / Year: 2018
Title: Structural Basis for Recognition of a Unique Epitope by a Human Anti-tau Antibody.
Authors: Zhang, H. / Zhu, X. / Pascual, G. / Wadia, J.S. / Keogh, E. / Hoozemans, J.J. / Siregar, B. / Inganas, H. / Stoop, E.J.M. / Goudsmit, J. / Apetri, A. / Koudstaal, W. / Wilson, I.A.
History
DepositionMar 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 25, 2019Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Heavy chain of CBTAU-24.1 antibody
L: Light chain (kappa) of CBTAU-24.1 antibody
R: phosphorylated tau peptide
A: Heavy chain of CBTAU-24.1 antibody
B: Light chain (kappa) of CBTAU-24.1 antibody
C: phosphorylated tau peptide
D: Heavy chain of CBTAU-24.1 antibody
E: Light chain (kappa) of CBTAU-24.1 antibody
F: phosphorylated tau peptide
H: Heavy chain of CBTAU-24.1 antibody
I: Light chain (kappa) of CBTAU-24.1 antibody
J: phosphorylated tau peptide
K: Heavy chain of CBTAU-24.1 antibody
M: Light chain (kappa) of CBTAU-24.1 antibody
N: phosphorylated tau peptide
O: Heavy chain of CBTAU-24.1 antibody
P: Light chain (kappa) of CBTAU-24.1 antibody
Q: phosphorylated tau peptide


Theoretical massNumber of molelcules
Total (without water)297,45018
Polymers297,45018
Non-polymers00
Water7,386410
1
G: Heavy chain of CBTAU-24.1 antibody
L: Light chain (kappa) of CBTAU-24.1 antibody
R: phosphorylated tau peptide


Theoretical massNumber of molelcules
Total (without water)49,5753
Polymers49,5753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-35 kcal/mol
Surface area20040 Å2
MethodPISA
2
A: Heavy chain of CBTAU-24.1 antibody
B: Light chain (kappa) of CBTAU-24.1 antibody
C: phosphorylated tau peptide


Theoretical massNumber of molelcules
Total (without water)49,5753
Polymers49,5753
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-37 kcal/mol
Surface area19960 Å2
MethodPISA
3
D: Heavy chain of CBTAU-24.1 antibody
E: Light chain (kappa) of CBTAU-24.1 antibody
F: phosphorylated tau peptide


Theoretical massNumber of molelcules
Total (without water)49,5753
Polymers49,5753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-37 kcal/mol
Surface area19990 Å2
MethodPISA
4
H: Heavy chain of CBTAU-24.1 antibody
I: Light chain (kappa) of CBTAU-24.1 antibody
J: phosphorylated tau peptide


Theoretical massNumber of molelcules
Total (without water)49,5753
Polymers49,5753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-35 kcal/mol
Surface area19980 Å2
MethodPISA
5
K: Heavy chain of CBTAU-24.1 antibody
M: Light chain (kappa) of CBTAU-24.1 antibody
N: phosphorylated tau peptide


Theoretical massNumber of molelcules
Total (without water)49,5753
Polymers49,5753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-38 kcal/mol
Surface area20210 Å2
MethodPISA
6
O: Heavy chain of CBTAU-24.1 antibody
P: Light chain (kappa) of CBTAU-24.1 antibody
Q: phosphorylated tau peptide


Theoretical massNumber of molelcules
Total (without water)49,5753
Polymers49,5753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-38 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.353, 107.811, 107.931
Angle α, β, γ (deg.)62.16, 71.02, 90.77
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
Heavy chain of CBTAU-24.1 antibody


Mass: 24141.000 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
Light chain (kappa) of CBTAU-24.1 antibody


Mass: 24419.986 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide
phosphorylated tau peptide


Mass: 1014.029 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 50% (v/v) MPD, 0.2M (NH4)H2PO4, 0.1M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 88890 / % possible obs: 91.1 % / Redundancy: 3.4 % / CC1/2: 0.9 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.094 / Rrim(I) all: 0.182 / Net I/σ(I): 8.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3914 / CC1/2: 0.65 / Rpim(I) all: 0.351 / Rrim(I) all: 0.637 / % possible all: 79.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q9Q

4q9q


Resolution: 2.603→46.864 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 4623 5.21 %
Rwork0.1995 --
obs0.2021 88708 90.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.603→46.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20418 0 0 410 20828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01320946
X-RAY DIFFRACTIONf_angle_d1.13128577
X-RAY DIFFRACTIONf_dihedral_angle_d12.53112477
X-RAY DIFFRACTIONf_chiral_restr0.0593213
X-RAY DIFFRACTIONf_plane_restr0.013632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6028-2.63240.31481030.27942280X-RAY DIFFRACTION72
2.6324-2.66340.33241210.26672461X-RAY DIFFRACTION80
2.6634-2.69590.36861410.26952623X-RAY DIFFRACTION82
2.6959-2.730.32041280.26292549X-RAY DIFFRACTION84
2.73-2.76590.34471520.28032790X-RAY DIFFRACTION89
2.7659-2.80380.34751530.26582732X-RAY DIFFRACTION89
2.8038-2.84380.33611240.25212887X-RAY DIFFRACTION91
2.8438-2.88630.33031510.24772840X-RAY DIFFRACTION93
2.8863-2.93140.2921370.23692934X-RAY DIFFRACTION93
2.9314-2.97940.29551520.24242840X-RAY DIFFRACTION92
2.9794-3.03080.30251500.23762822X-RAY DIFFRACTION92
3.0308-3.08590.3241440.23472837X-RAY DIFFRACTION89
3.0859-3.14520.30231520.23592501X-RAY DIFFRACTION83
3.1452-3.20940.28831670.22712903X-RAY DIFFRACTION94
3.2094-3.27920.25341440.21643024X-RAY DIFFRACTION97
3.2792-3.35540.30121680.22073022X-RAY DIFFRACTION97
3.3554-3.43930.27291940.21212942X-RAY DIFFRACTION96
3.4393-3.53230.26172020.20142869X-RAY DIFFRACTION95
3.5323-3.63620.26361800.18962956X-RAY DIFFRACTION96
3.6362-3.75350.22531400.18882988X-RAY DIFFRACTION95
3.7535-3.88760.24831540.18432864X-RAY DIFFRACTION94
3.8876-4.04320.22641260.18122739X-RAY DIFFRACTION88
4.0432-4.22710.21021470.16972652X-RAY DIFFRACTION86
4.2271-4.44980.20561910.14972996X-RAY DIFFRACTION97
4.4498-4.72830.18031680.1393006X-RAY DIFFRACTION97
4.7283-5.0930.19021730.14352947X-RAY DIFFRACTION96
5.093-5.60480.18891600.16292841X-RAY DIFFRACTION93
5.6048-6.4140.21681500.18722600X-RAY DIFFRACTION84
6.414-8.07430.2081920.19652937X-RAY DIFFRACTION96
8.0743-46.87140.19351590.18952703X-RAY DIFFRACTION88

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