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- PDB-2x6m: Structure of a single domain camelid antibody fragment in complex... -

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Basic information

Entry
Database: PDB / ID: 2x6m
TitleStructure of a single domain camelid antibody fragment in complex with a C-terminal peptide of alpha-synuclein
Components
  • ALPHA-SYNUCLEIN PEPTIDE
  • HEAVY CHAIN VARIABLE DOMAIN FROM DROMEDARY
KeywordsIMMUNE SYSTEM / PARKINSON'S DISEASE / ALZHEIMER DISEASE AMYLOID / NANOBODY / AFFINITY TAG
Function / homology
Function and homology information


negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of synaptic vesicle recycling / regulation of reactive oxygen species biosynthetic process / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of norepinephrine uptake / transporter regulator activity / regulation of locomotion / mitochondrial ATP synthesis coupled electron transport / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / negative regulation of microtubule polymerization / synaptic vesicle transport / positive regulation of receptor recycling / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / dynein complex binding / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / positive regulation of endocytosis / positive regulation of exocytosis / response to magnesium ion / synaptic vesicle exocytosis / enzyme inhibitor activity / kinesin binding / synaptic vesicle endocytosis / regulation of presynapse assembly / response to type II interferon / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / alpha-tubulin binding / supramolecular fiber organization / inclusion body / phospholipid metabolic process / cellular response to copper ion / axon terminus / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / regulation of microtubule cytoskeleton organization / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / negative regulation of protein kinase activity / excitatory postsynaptic potential / fatty acid metabolic process / phosphoprotein binding / protein tetramerization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / protein destabilization / PKR-mediated signaling / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / actin binding / growth cone / cell cortex / cellular response to oxidative stress / neuron apoptotic process / chemical synaptic transmission / molecular adaptor activity / negative regulation of neuron apoptotic process / response to lipopolysaccharide / histone binding / amyloid fibril formation / lysosome / oxidoreductase activity / postsynapse / transcription cis-regulatory region binding / positive regulation of apoptotic process / Amyloid fiber formation / copper ion binding / response to xenobiotic stimulus / axon / neuronal cell body
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCAMELUS DROMEDARIUS (Arabian camel)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsDeGenst, E. / Guilliams, T. / Wellens, J. / O'Day, E.M. / Waudby, C.A. / Meehan, S. / Dumoulin, M. / Hsu, S.-T.D. / Cremades, N. / Verschueren, K.H.G. ...DeGenst, E. / Guilliams, T. / Wellens, J. / O'Day, E.M. / Waudby, C.A. / Meehan, S. / Dumoulin, M. / Hsu, S.-T.D. / Cremades, N. / Verschueren, K.H.G. / Pardon, E. / Wyns, L. / Steyaert, J. / Christodoulou, J. / Dobson, C.M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure and Properties of a Complex of Alpha-Synuclein and a Single-Domain Camelid Antibody.
Authors: De Genst, E.J. / Guilliams, T. / Wellens, J. / O'Day, E.M. / Waudby, C.A. / Meehan, S. / Dumoulin, M. / Hsu, S.-T.D. / Cremades, N. / Verschueren, K.H.G. / Pardon, E. / Wyns, L. / Steyaert, ...Authors: De Genst, E.J. / Guilliams, T. / Wellens, J. / O'Day, E.M. / Waudby, C.A. / Meehan, S. / Dumoulin, M. / Hsu, S.-T.D. / Cremades, N. / Verschueren, K.H.G. / Pardon, E. / Wyns, L. / Steyaert, J. / Christodoulou, J. / Dobson, C.M.
History
DepositionFeb 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references / Structure summary / Version format compliance
Revision 1.2Mar 29, 2017Group: Other
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 13, 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
A: HEAVY CHAIN VARIABLE DOMAIN FROM DROMEDARY
B: ALPHA-SYNUCLEIN PEPTIDE


Theoretical massNumber of molelcules
Total (without water)14,5092
Polymers14,5092
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-0.8 kcal/mol
Surface area6540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.170, 63.120, 62.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

21A-2078-

HOH

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Components

#1: Antibody HEAVY CHAIN VARIABLE DOMAIN FROM DROMEDARY


Mass: 13437.815 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ENGINEERED FROM IMMUNISED DROMEDARY / Source: (gene. exp.) CAMELUS DROMEDARIUS (Arabian camel) / Tissue: BLOOD / Cell: LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WK6
#2: Protein/peptide ALPHA-SYNUCLEIN PEPTIDE


Mass: 1071.052 Da / Num. of mol.: 1
Fragment: C-TERMINAL FRAGMENT OF ALPHA-SYNUCLEIN, RESIDUES 132-140
Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P37840
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.01 Å3/Da / Density % sol: 38.84 % / Description: NONE
Crystal growpH: 7.5 / Details: 25% PEG6000, 100 MM HEPES PH 7.5, 100 MM LICL

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 1.62→30 Å / Num. obs: 15482 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 18.126 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 23.3
Reflection shellResolution: 1.62→1.71 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HCV

1hcv


Resolution: 1.62→43.56 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.577 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20258 1101 7.1 %RANDOM
Rwork0.15634 ---
obs0.1596 14361 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.62→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 0 0 208 1201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9381446
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0315147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15423.87849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93115166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.031157
X-RAY DIFFRACTIONr_chiral_restr0.1470.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021843
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_it1.5311.5671
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.48121068
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5613389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5394.5369
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: 1.623→1.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 87 -
Rwork0.318 1032 -
obs--99.73 %
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)
10.7485-0.26390.45410.6799-0.29910.6967-0.01060.02520.02360.0086-0.02890.02360.0076-0.01190.03950.0291-0.0045-0.00790.0268-0.00620.0243-15.045914.95079.2345
217.2343-0.81233.8938-1.2996-0.54270.7132-0.0793-0.1768-0.25080.05980.03640.04540.0898-0.14310.04290.0004-0.0326-0.01210.0872-0.00850.0791-34.658815.21963.5248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 127
2X-RAY DIFFRACTION2B4 - 9

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