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- PDB-8zvy: Alpha-Synuclein with H2a-H2b dimer complex structure. -

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Basic information

Entry
Database: PDB / ID: 8zvy
TitleAlpha-Synuclein with H2a-H2b dimer complex structure.
Components
  • Histone H2B 1.1,Histone H2A type 1
  • Isoform 1 of Alpha-synuclein
KeywordsNUCLEAR PROTEIN / Parkinson's disease / histone chaperone / alpha-synuclein / H2a-H2b dimer / (H3-H4)2 tetramer / Neurodegeneration
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 / structural constituent of chromatin / nucleosome / heterochromatin formation / 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
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain ...Synuclein / Alpha-synuclein / Synuclein / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Alpha-synuclein
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsPadavattan, S. / Jos, S. / Kambaru, A.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)ECR/2018/002219 India
CitationJournal: Commun Biol / Year: 2025
Title: Structural and functional insights into the nuclear role of Parkinson's disease-associated alpha-synuclein as a histone chaperone.
Authors: Jos, S. / Kambaru, A. / Prasad, T.K. / Parthasarathi, S. / Kamariah, N. / Nath, S. / Padmanabhan, B. / Padavattan, S.
History
DepositionJun 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H2B 1.1,Histone H2A type 1
B: Histone H2B 1.1,Histone H2A type 1
C: Isoform 1 of Alpha-synuclein
D: Isoform 1 of Alpha-synuclein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8476
Polymers45,7764
Non-polymers712
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, The binding between Alpha-Synuclein peptide and Histone H2a-H2b dimer was analysed using EDC- and DSS-mediated cross-linking., isothermal titration calorimetry, Biophysical ...Evidence: cross-linking, The binding between Alpha-Synuclein peptide and Histone H2a-H2b dimer was analysed using EDC- and DSS-mediated cross-linking., isothermal titration calorimetry, Biophysical studies such as ITC and MicroScale thermophoresis (MST) were performed to quantify the binding interactions between Alpha-Synuclein and Histone H2a-H2b dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-17 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.005, 68.240, 102.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 37 through 56 or resid 58...
d_2ens_1(chain "B" and (resid 37 through 56 or resid 58...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERSERSERAA37 - 565 - 24
d_12LYSLYSMETMETAA58 - 6026 - 28
d_13ILEILEMETMETAA62 - 6330 - 31
d_14PHEPHEVALVALAA66 - 6734 - 35
d_15ASPASPPHEPHEAA69 - 7137 - 39
d_16ARGARGTHRTHRAA73 - 9141 - 59
d_17ARGARGLEULEUAA93 - 10161 - 69
d_18LEULEUGLUGLUAA103 - 10671 - 74
d_19ALAALAGLYGLYAA108 - 11576 - 83
d_110LYSLYSTHRTHRAA117 - 110285 - 183
d_21SERSERSERSERBB37 - 565 - 24
d_22LYSLYSMETMETBB58 - 6026 - 28
d_23ILEILEMETMETBB62 - 6330 - 31
d_24PHEPHEVALVALBB66 - 6734 - 35
d_25ASPASPPHEPHEBB69 - 7137 - 39
d_26ARGARGTHRTHRBB73 - 9141 - 59
d_27ARGARGLEULEUBB93 - 10161 - 69
d_28LEULEUGLUGLUBB103 - 10671 - 74
d_29ALAALAGLYGLYBB108 - 11576 - 83
d_210LYSLYSTHRTHRBB117 - 110285 - 183

NCS oper: (Code: givenMatrix: (0.563830745708, -0.74523461808, -0.355977884438), (0.736463557724, 0.648753621609, -0.191677245898), (0.373786460883, -0.154091214755, 0.914625376422)Vector: 18. ...NCS oper: (Code: given
Matrix: (0.563830745708, -0.74523461808, -0.355977884438), (0.736463557724, 0.648753621609, -0.191677245898), (0.373786460883, -0.154091214755, 0.914625376422)
Vector: 18.3064624572, -6.68472953237, -23.8872756249)

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Components

#1: Protein Histone H2B 1.1,Histone H2A type 1 / H2B1.1


Mass: 20521.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Histone H2a-H2b dimer / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281, UniProt: P06897
#2: Protein/peptide Isoform 1 of Alpha-synuclein / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


Mass: 2366.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Alpha-Synuclein peptide (121-140) / Source: (synth.) Homo sapiens (human) / References: UniProt: P37840
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.34 % / Description: solid
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Tris pH 8.0 and 10% PEG 8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.72→68.24 Å / Num. obs: 46279 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 34.36 Å2 / CC1/2: 1 / Net I/σ(I): 37.1
Reflection shellResolution: 1.72→1.75 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2444 / CC1/2: 0.879

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6w4l

6w4l


Resolution: 1.72→45.48 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2203 2316 5.02 %
Rwork0.1906 43814 -
obs0.1921 46130 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.62 Å2
Refinement stepCycle: LAST / Resolution: 1.72→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3003 0 2 228 3233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653111
X-RAY DIFFRACTIONf_angle_d0.88564215
X-RAY DIFFRACTIONf_chiral_restr0.0536483
X-RAY DIFFRACTIONf_plane_restr0.0097544
X-RAY DIFFRACTIONf_dihedral_angle_d16.1421201
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.50759650669 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.36831330.3142553X-RAY DIFFRACTION99.63
1.76-1.790.28611330.27322571X-RAY DIFFRACTION99.96
1.79-1.840.29331290.24792516X-RAY DIFFRACTION100
1.84-1.880.27131450.2272528X-RAY DIFFRACTION99.85
1.88-1.930.32551320.272505X-RAY DIFFRACTION98.4
1.93-1.990.3031350.24372568X-RAY DIFFRACTION99.89
1.99-2.050.30651330.23622553X-RAY DIFFRACTION100
2.05-2.130.24691130.21322551X-RAY DIFFRACTION99.25
2.13-2.210.26091400.19592567X-RAY DIFFRACTION100
2.21-2.310.25171390.19452537X-RAY DIFFRACTION99.66
2.31-2.430.21931270.18352590X-RAY DIFFRACTION100
2.43-2.590.23211440.18732574X-RAY DIFFRACTION100
2.59-2.790.24321370.21032595X-RAY DIFFRACTION99.93
2.79-3.070.24581470.20282585X-RAY DIFFRACTION100
3.07-3.510.23491460.19862602X-RAY DIFFRACTION100
3.51-4.420.16811520.16232639X-RAY DIFFRACTION100
4.42-45.480.18381310.16812780X-RAY DIFFRACTION99.83
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)
13.26323822780.57809520670.3291441137922.58293639185-0.004182537859312.87307769392-0.1261634141870.1986980611250.573028408094-0.1804643088590.0380986635718-0.0809800783914-0.4889107384450.0844988379947-0.01459261152760.2938087792580.00755710775954-0.02122765247680.1627834650920.002448113367140.314808811099-3.682987088674.8046100924513.4394913318
21.80270509835-0.386934045015-0.06143486708153.21841638751-0.6691823468233.056638589490.0114459072628-0.05065142015280.1375981248750.0660096394713-0.0532313279329-0.0255164038142-0.20309993521-0.1446664453850.03923508639270.138622106507-0.0190476488980.001153068522840.242394335842-0.005492822515770.2271225419078.00086659127-8.77557588943-13.6707323148
33.6248040306-2.439830976193.004900621545.43556368555-3.762707142678.14712354336-0.8313625933050.3846633475470.886491564822-1.303431990871.306322330191.21887082142-0.923683125041-0.632828904969-0.6376942980871.49935430985-0.217995613407-0.31511265270.7510927836030.08255659993821.1674966271-2.4534375224825.178399492910.0438568678
43.29972212747-1.345411852412.731260643747.07444803335-4.418668424523.945260038180.05506242803510.0968063194325-0.266466168743-0.381047747417-0.297930747128-1.401841424141.218622854021.702219011850.1374186111950.6692062633030.186813776327-0.02804056526650.7499149764690.0504102297910.756686781365-0.7953259520684.70321158719-35.3912639634
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 35:1103)AA35 - 11031 - 182
22(chain B and resseq 36:1102)BB36 - 11021 - 180
33(chain C and resseq 130:140)CC131 - 1401 - 10
44(chain D and resseq 127:140)DD128 - 1401 - 13

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