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- PDB-8qf5: Complex between N-lobe of Arc and nanobody E5 -

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Basic information

Entry
Database: PDB / ID: 8qf5
TitleComplex between N-lobe of Arc and nanobody E5
Components
  • Activity-regulated cytoskeleton-associated protein
  • Nanobody E5
KeywordsIMMUNE SYSTEM / nanobody
Function / homology
Function and homology information


postsynaptic endosome / virus-like capsid / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / NGF-stimulated transcription / dendritic spine morphogenesis / regulation of cell morphogenesis ...postsynaptic endosome / virus-like capsid / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / NGF-stimulated transcription / dendritic spine morphogenesis / regulation of cell morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / regulation of long-term synaptic potentiation / response to morphine / anterior/posterior pattern specification / regulation of long-term synaptic depression / regulation of neuronal synaptic plasticity / mRNA transport / long-term memory / cytoskeleton organization / acrosomal vesicle / learning / long-term synaptic potentiation / postsynaptic density membrane / modulation of chemical synaptic transmission / protein homooligomerization / endocytosis / extracellular vesicle / cell migration / actin cytoskeleton / cell cortex / early endosome membrane / response to ethanol / dendritic spine / membrane raft / mRNA binding / neuronal cell body / glutamatergic synapse / structural molecule activity / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Activity-regulated cytoskeleton-associated protein, capsid domain / Activity-regulated cytoskeleton-associated protein / Activity-regulated cytoskeleton-associated protein, C-terminal domain / Activity-regulated cytoskeleton-associated protein, N-terminal domain / Arc C-lobe / Arc MA domain
Similarity search - Domain/homology
Activity-regulated cytoskeleton-associated protein
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGodoy Munoz, J.M. / Kursula, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Complex between N-lobe of Arc and nanobody E5
Authors: Godoy Munoz, J.M. / Kursula, P.
History
DepositionSep 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Nanobody E5
H: Activity-regulated cytoskeleton-associated protein
A: Nanobody E5
B: Activity-regulated cytoskeleton-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5299
Polymers43,2624
Non-polymers2675
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.500, 99.480, 138.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11H-301-

ZN

21B-441-

HOH

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Components

#1: Antibody Nanobody E5


Mass: 12767.269 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Activity-regulated cytoskeleton-associated protein / hArc / Activity-regulated gene 3.1 protein homolog / ARC/ARG3.1 / Arg3.1


Mass: 8863.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARC, KIAA0278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7LC44
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8, 0.01 M ZnCl2 and 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 146561 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.052 / Net I/σ(I): 10.8
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 2.496 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 14662 / CC1/2: 0.194 / Rrim(I) all: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→33.83 Å / SU ML: 0.253 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1926 3780 2.59 %
Rwork0.1445 142056 -
obs0.1457 145836 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.96 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 5 346 3331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01133096
X-RAY DIFFRACTIONf_angle_d1.09454184
X-RAY DIFFRACTIONf_chiral_restr0.0823420
X-RAY DIFFRACTIONf_plane_restr0.0099549
X-RAY DIFFRACTIONf_dihedral_angle_d15.97111126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.38171330.36244850X-RAY DIFFRACTION93.3
1.52-1.540.36481390.33625133X-RAY DIFFRACTION97.04
1.54-1.560.31681410.32445318X-RAY DIFFRACTION98.7
1.56-1.580.33221420.31165270X-RAY DIFFRACTION98.96
1.58-1.610.35391400.30935231X-RAY DIFFRACTION99.33
1.61-1.630.36981410.29135314X-RAY DIFFRACTION99.24
1.63-1.660.4321420.29065311X-RAY DIFFRACTION99.56
1.66-1.690.3511410.25665253X-RAY DIFFRACTION99.12
1.69-1.720.31991380.23415258X-RAY DIFFRACTION98.54
1.72-1.750.24361410.22035172X-RAY DIFFRACTION97.41
1.75-1.790.24881360.1845186X-RAY DIFFRACTION97.81
1.79-1.820.24811440.1625361X-RAY DIFFRACTION100
1.82-1.870.21541390.14975260X-RAY DIFFRACTION99.98
1.87-1.910.23421470.15045402X-RAY DIFFRACTION99.93
1.91-1.970.19911380.15415190X-RAY DIFFRACTION99.85
1.97-2.020.23011400.11845419X-RAY DIFFRACTION99.89
2.02-2.090.16781390.11395233X-RAY DIFFRACTION99.94
2.09-2.160.19651430.1195391X-RAY DIFFRACTION99.91
2.16-2.250.17911420.11135224X-RAY DIFFRACTION99.67
2.25-2.350.17861440.12735271X-RAY DIFFRACTION98.89
2.35-2.480.19771380.12625213X-RAY DIFFRACTION97.36
2.48-2.630.21211360.13645336X-RAY DIFFRACTION99.82
2.63-2.830.20951380.12435285X-RAY DIFFRACTION99.93
2.83-3.120.18571380.14455326X-RAY DIFFRACTION99.76
3.12-3.570.16381390.12645264X-RAY DIFFRACTION99.69
3.57-4.50.15531390.12855316X-RAY DIFFRACTION99.71
4.5-33.830.17531420.15395269X-RAY DIFFRACTION98.92

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