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- PDB-6ct7: Fab of anti-a-synuclein antibody BIIB054 in complex with acetylat... -

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Basic information

Entry
Database: PDB / ID: 6ct7
TitleFab of anti-a-synuclein antibody BIIB054 in complex with acetylated a-synuclein peptide (1-10)
Components
  • ACE-MET-ASP-VAL-PHE-MET-LYS-GLY-LEU-SER-LYS
  • BIIB054 Fab heavy chain
  • BIIB054 Fab light chain
KeywordsIMMUNE SYSTEM / Fab / complex / a-synuclein / Parkinson disease
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 / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / regulation of synaptic vesicle recycling ...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 / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / regulation of synaptic vesicle recycling / negative regulation of chaperone-mediated autophagy / mitochondrial membrane organization / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / negative regulation of platelet-derived growth factor receptor signaling pathway / regulation of glutamate secretion / Lewy body / dopamine biosynthetic process / response to iron(II) ion / negative regulation of thrombin-activated receptor signaling pathway / SNARE complex assembly / positive regulation of neurotransmitter secretion / negative regulation of dopamine metabolic process / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / regulation of locomotion / negative regulation of microtubule polymerization / regulation of norepinephrine uptake / synaptic vesicle priming / transporter regulator activity / synaptic vesicle transport / protein kinase inhibitor activity / dopamine uptake involved in synaptic transmission / regulation of dopamine secretion / mitochondrial ATP synthesis coupled electron transport / positive regulation of receptor recycling / dynein complex binding / cuprous ion binding / nuclear outer membrane / response to magnesium ion / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / negative regulation of serotonin uptake / response to type II interferon / synaptic vesicle endocytosis / kinesin binding / regulation of presynapse assembly / cysteine-type endopeptidase inhibitor activity / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / supramolecular fiber organization / cellular response to fibroblast growth factor stimulus / phospholipid metabolic process / inclusion body / cellular response to epinephrine stimulus / Hsp70 protein binding / enzyme inhibitor activity / axon terminus / response to interleukin-1 / regulation of microtubule cytoskeleton organization / cellular response to copper ion / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / adult locomotory behavior / glutathione metabolic process / excitatory postsynaptic potential / protein tetramerization / protein sequestering activity / tubulin binding / phosphoprotein binding / microglial cell activation / ferrous iron binding / fatty acid metabolic process / synapse organization / PKR-mediated signaling / regulation of long-term neuronal synaptic plasticity / receptor internalization / phospholipid binding / protein destabilization / tau protein binding / enzyme activator activity / terminal bouton / positive regulation of inflammatory response / long-term synaptic potentiation / synaptic vesicle membrane / actin cytoskeleton / growth cone / actin binding / neuron apoptotic process / cellular response to oxidative stress / cell cortex / histone binding / response to lipopolysaccharide / microtubule binding / amyloid fibril formation / chemical synaptic transmission
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Alpha-synuclein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsArndt, J.W.
CitationJournal: Neurobiol. Dis. / Year: 2018
Title: Development of an aggregate-selective, human-derived alpha-synuclein antibody BIIB054 that ameliorates disease phenotypes in Parkinson's disease models.
Authors: Weihofen, A. / Liu, Y. / Arndt, J.W. / Huy, C. / Quan, C. / Smith, B.A. / Baeriswyl, J.L. / Cavegn, N. / Senn, L. / Su, L. / Marsh, G. / Auluck, P.K. / Montrasio, F. / Nitsch, R.M. / Hirst, ...Authors: Weihofen, A. / Liu, Y. / Arndt, J.W. / Huy, C. / Quan, C. / Smith, B.A. / Baeriswyl, J.L. / Cavegn, N. / Senn, L. / Su, L. / Marsh, G. / Auluck, P.K. / Montrasio, F. / Nitsch, R.M. / Hirst, W.D. / Cedarbaum, J.M. / Pepinsky, R.B. / Grimm, J. / Weinreb, P.H.
History
DepositionMar 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 16, 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: BIIB054 Fab light chain
H: BIIB054 Fab heavy chain
S: ACE-MET-ASP-VAL-PHE-MET-LYS-GLY-LEU-SER-LYS
B: BIIB054 Fab light chain
A: BIIB054 Fab heavy chain
T: ACE-MET-ASP-VAL-PHE-MET-LYS-GLY-LEU-SER-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,02410
Polymers94,7846
Non-polymers2404
Water9,566531
1
L: BIIB054 Fab light chain
H: BIIB054 Fab heavy chain
S: ACE-MET-ASP-VAL-PHE-MET-LYS-GLY-LEU-SER-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5726
Polymers47,3923
Non-polymers1803
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-22 kcal/mol
Surface area19270 Å2
MethodPISA
2
B: BIIB054 Fab light chain
A: BIIB054 Fab heavy chain
T: ACE-MET-ASP-VAL-PHE-MET-LYS-GLY-LEU-SER-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4524
Polymers47,3923
Non-polymers601
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-29 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.849, 101.492, 73.400
Angle α, β, γ (deg.)90.00, 117.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody BIIB054 Fab light chain


Mass: 22893.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody BIIB054 Fab heavy chain


Mass: 23315.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide ACE-MET-ASP-VAL-PHE-MET-LYS-GLY-LEU-SER-LYS


Mass: 1183.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: acetylated peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P37840*PLUS
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: 18% w/v PEG 3350, 17% w/v PEG 400, 4.8% v/v 2-propanol, and 100 mM CAPSO pH 8.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 72048 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 5.3
Reflection shellResolution: 1.9→1.9715 Å / Rsym value: 0.643

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.903→24.86 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.23
RfactorNum. reflection% reflection
Rfree0.2229 3429 4.76 %
Rwork0.1798 --
obs0.1819 72048 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.903→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 16 532 7016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076648
X-RAY DIFFRACTIONf_angle_d0.9539073
X-RAY DIFFRACTIONf_dihedral_angle_d7.4394291
X-RAY DIFFRACTIONf_chiral_restr0.0551034
X-RAY DIFFRACTIONf_plane_restr0.0061161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9034-1.93060.3986810.38591542X-RAY DIFFRACTION53
1.9306-1.95940.38811410.3452590X-RAY DIFFRACTION88
1.9594-1.990.29331280.24752741X-RAY DIFFRACTION93
1.99-2.02270.23991430.19282867X-RAY DIFFRACTION98
2.0227-2.05750.21791270.19682949X-RAY DIFFRACTION100
2.0575-2.09490.21891640.19422911X-RAY DIFFRACTION100
2.0949-2.13520.23371550.18562892X-RAY DIFFRACTION100
2.1352-2.17870.2051730.16672926X-RAY DIFFRACTION100
2.1787-2.22610.20371380.16552992X-RAY DIFFRACTION100
2.2261-2.27780.26611510.19922910X-RAY DIFFRACTION100
2.2778-2.33480.23141600.16442893X-RAY DIFFRACTION100
2.3348-2.39780.20771820.15852924X-RAY DIFFRACTION100
2.3978-2.46830.23491240.16022935X-RAY DIFFRACTION100
2.4683-2.54790.22591460.1642981X-RAY DIFFRACTION100
2.5479-2.63890.26281250.17692931X-RAY DIFFRACTION100
2.6389-2.74440.21191050.17752974X-RAY DIFFRACTION100
2.7444-2.86920.24171730.19912906X-RAY DIFFRACTION100
2.8692-3.02020.29561480.20462953X-RAY DIFFRACTION100
3.0202-3.2090.22541420.19232962X-RAY DIFFRACTION100
3.209-3.45620.22191120.19312984X-RAY DIFFRACTION100
3.4562-3.80290.20881710.18042931X-RAY DIFFRACTION100
3.8029-4.35070.1951570.16742956X-RAY DIFFRACTION100
4.3507-5.47170.18261290.14362967X-RAY DIFFRACTION100
5.4717-24.86190.20251540.16273002X-RAY DIFFRACTION99
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)
10.4162-0.1975-0.32080.6958-0.11621.0543-0.05380.15310.0194-0.1022-0.0571-0.03170.0032-0.4186-0.00030.1570.0133-0.01050.2649-0.01790.15324.43086.7934.6033
20.4380.1025-0.00330.2529-0.05630.1543-0.05580.0964-0.08570.00920.08240.06710.11170.2631-0.03930.1782-0.0043-0.0570.3116-0.00860.1806-23.5242-8.727325.9201
30.6983-0.24820.59780.3116-0.53370.9037-0.0180.05310.1705-0.05620.02220.096-0.09960.0058-0.00010.17980.01-0.01480.20730.00090.188-27.3614-3.432224.5093
40.44160.15550.1170.19-0.20320.28830.1161-0.1328-0.0055-0.129-0.0251-0.1585-0.14670.10230.00020.1667-0.01510.03450.17380.00980.23237.2671.687230.3402
50.05290.02820.05990.12910.04880.0513-0.1309-0.2177-0.021-0.02160.0386-0.30780.26070.5305-0.00050.25170.06910.04470.25490.00890.270418.94441.273922.1695
60.0050.03530.0370.21980.0090.16870.00480.30610.03910.0121-0.10020.20030.0371-0.30280.00010.12210.00770.00630.1982-0.02680.21584.06157.738320.9683
70.096-0.0846-0.09740.1116-0.01460.5018-0.1004-0.00930.12420.0475-0.0043-0.0798-0.24930.2067-0.00110.13280.0088-0.01090.16490.01450.159117.168711.468624.3848
80.14540.1954-0.07240.2183-0.19730.53440.12270.07540.0523-0.0099-0.12670.02380.0642-0.0549-00.11970.0118-0.04170.0899-0.01250.13368.1247.533728.7269
90.0296-0.0088-0.01950.0714-0.13310.10060.08120.09930.1314-0.0285-0.028-0.02150.1404-0.1717-0.00040.1663-0.00380.02120.1897-0.03760.20921.20751.571229.5668
100.116-0.14660.0140.1292-0.02430.0248-0.14560.1364-0.1942-0.30620.06650.2246-0.0665-0.24910.00550.146-0.0106-0.04940.2445-0.0770.2172-24.4135-17.123829.3261
110.3612-0.00420.1276-0.04340.04950.51530.0758-0.42860.2463-0.1167-0.0177-0.1005-0.0041-0.09530.0970.13790.00790.02540.1338-0.06220.1806-12.084-11.527431.6891
120.2386-0.19790.18480.179-0.24630.1632-0.0911-0.03160.1032-0.0815-0.02930.17950.08490.0517-0.00010.1770.00850.01340.1958-0.03190.2139-13.1213-6.975128.1154
130.2285-0.0374-0.2630.02670.0540.17610.1236-0.1356-0.2033-0.048-0.0883-0.22-0.0052-0.0653-00.1617-0.00490.00830.1664-0.00580.2418-14.1242-19.179630.6347
140.0751-0.0636-0.11170.04430.11480.09480.0617-0.3613-0.12880.4806-0.11420.25280.18240.08180.0060.21650.02710.06860.22130.03070.2869-13.6321-18.179438.201
150.06410.0094-0.10880.0203-0.01760.11110.08760.3671-0.5162-0.4558-0.0341-0.08850.07430.1258-0.01270.22680.0309-0.00930.2129-0.00670.280120.22744.40028.8933
160.32520.02950.13580.3410.22830.16220.07360.14690.1221-0.1938-0.065-0.06710.08210.1708-0.00020.2458-0.0016-0.00680.2119-0.01660.17511.9266-31.51533.7167
170.5409-0.16780.19180.2579-0.06910.53890.00220.0308-0.04010.0122-0.03710.0779-0.05060.015900.1757-0.0033-0.01540.159-0.00840.14492.1199-25.184710.1515
180.0469-0.1056-0.02910.6161-0.27210.35180.1393-0.34930.1762-0.106-0.0857-0.0428-0.0199-0.030500.2153-0.01380.03920.3175-0.03110.152731.587-11.6593-9.7953
190.33270.1980.04081.1710.01761.17620.083-0.1157-0.0775-0.10930.0678-0.07070.07250.03840.00010.25440.01380.0090.2167-0.01030.164830.9489-17.4273-13.3538
200.18890.3489-0.07810.4729-0.16840.2917-0.06950.02330.24930.045-0.0109-0.20940.0751-0.0032-0.00010.21420.0057-0.01470.1841-0.01470.237422.9962-20.81922.2787
210.0675-0.0816-0.13670.04510.02080.2355-0.072-0.1525-0.03880.09610.04730.0083-0.1116-0.0719-00.19840.02670.02240.129-0.00670.193111.2081-21.359329.2185
220.69990.0230.16820.3258-0.3730.36250.01740.00820.0183-0.0562-0.0071-0.02340.0394-0.026-00.13160.01340.01160.0924-0.01060.136717.0426-28.122423.3801
230.0318-0.0036-0.01410.0267-0.04460.0246-0.1619-0.05340.11-0.0999-0.00640.1423-0.0138-0.05770.00010.23260.00720.00480.16560.03610.213237.4799-21.965313.1582
240.0336-0.0108-0.03560.0352-0.01610.0273-0.0469-0.21120.1939-0.03130.0426-0.091-0.2396-0.06640.00010.22960.02580.00410.19090.02080.198735.1546-5.8471-4.8823
250.12210.11640.2980.1524-0.06310.63320.05240.00240.0213-0.1817-0.02310.06890.1191-0.06870.00010.15870.01080.01890.17410.02780.233430.4343-12.27233.657
260.0317-0.0366-0.03770.05110.01430.0818-0.00430.09950.1943-0.60170.1003-0.4623-0.05550.31830.00080.38830.00640.0310.24020.07420.272430.06142.2399-5.6187
270.2089-0.2916-0.04430.28490.11040.0964-0.0446-0.00250.02460.21880.0185-0.1761-0.33950.03030.00020.23210.01020.02840.19220.01730.189736.2439-4.37645.8589
28-0.0087-0.0145-0.0140.02130.06390.0172-0.0051-0.27440.04390.1796-0.06070.0557-0.1057-0.2772-00.19970.00760.00950.2002-0.00210.1731-1.1656-24.945924.2497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 107 )
2X-RAY DIFFRACTION2chain 'L' and (resid 108 through 131 )
3X-RAY DIFFRACTION3chain 'L' and (resid 132 through 212 )
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 17 )
5X-RAY DIFFRACTION5chain 'H' and (resid 18 through 33 )
6X-RAY DIFFRACTION6chain 'H' and (resid 34 through 45 )
7X-RAY DIFFRACTION7chain 'H' and (resid 46 through 78 )
8X-RAY DIFFRACTION8chain 'H' and (resid 79 through 99 )
9X-RAY DIFFRACTION9chain 'H' and (resid 100 through 119 )
10X-RAY DIFFRACTION10chain 'H' and (resid 120 through 134 )
11X-RAY DIFFRACTION11chain 'H' and (resid 135 through 157 )
12X-RAY DIFFRACTION12chain 'H' and (resid 158 through 177 )
13X-RAY DIFFRACTION13chain 'H' and (resid 178 through 203 )
14X-RAY DIFFRACTION14chain 'H' and (resid 204 through 214 )
15X-RAY DIFFRACTION15chain 'S' and (resid 0 through 10 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1 through 28 )
17X-RAY DIFFRACTION17chain 'B' and (resid 29 through 107 )
18X-RAY DIFFRACTION18chain 'B' and (resid 108 through 131 )
19X-RAY DIFFRACTION19chain 'B' and (resid 132 through 211 )
20X-RAY DIFFRACTION20chain 'A' and (resid 1 through 17 )
21X-RAY DIFFRACTION21chain 'A' and (resid 18 through 33 )
22X-RAY DIFFRACTION22chain 'A' and (resid 34 through 109 )
23X-RAY DIFFRACTION23chain 'A' and (resid 110 through 119 )
24X-RAY DIFFRACTION24chain 'A' and (resid 120 through 143 )
25X-RAY DIFFRACTION25chain 'A' and (resid 144 through 177 )
26X-RAY DIFFRACTION26chain 'A' and (resid 178 through 194 )
27X-RAY DIFFRACTION27chain 'A' and (resid 195 through 214 )
28X-RAY DIFFRACTION28chain 'T' and (resid 0 through 10 )

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