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- PDB-8qf4: Complex between N-lobe of Arc and nanobody H11 -

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Basic information

Entry
Database: PDB / ID: 8qf4
TitleComplex between N-lobe of Arc and nanobody H11
Components
  • Activity-regulated cytoskeleton-associated protein
  • Nanobody H11
KeywordsIMMUNE SYSTEM / nanobody
Function / homology
Function and homology information


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 long-term synaptic potentiation ...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 long-term synaptic potentiation / anterior/posterior pattern specification / regulation of postsynaptic neurotransmitter receptor internalization / regulation of neuronal synaptic plasticity / long-term memory / mRNA transport / regulation of long-term synaptic depression / cytoskeleton organization / acrosomal vesicle / protein homooligomerization / modulation of chemical synaptic transmission / long-term synaptic potentiation / endocytosis / cell migration / extracellular vesicle / actin cytoskeleton / early endosome membrane / cell cortex / dendritic spine / postsynaptic membrane / postsynaptic density / membrane raft / neuronal cell body / mRNA binding / glutamatergic synapse / structural molecule activity / plasma membrane / cytoplasm / cytosol
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
PHOSPHATE ION / Activity-regulated cytoskeleton-associated protein
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsGodoy Munoz, J.M. / Kursula, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Complex between Arc N-lobe and nanobody H11
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

Downloads & links

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Assembly

Deposited unit
E: Nanobody H11
A: Activity-regulated cytoskeleton-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1324
Polymers22,9422
Non-polymers1902
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-22 kcal/mol
Surface area9930 Å2
Unit cell
Length a, b, c (Å)41.820, 52.070, 44.220
Angle α, β, γ (deg.)90.000, 109.890, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody Nanobody H11


Mass: 14078.622 Da / Num. of mol.: 1
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.: 1
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M potassium phosphate citrate pH 4.2, 0.2 M NaCl and 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.83 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 1.02→50 Å / Num. obs: 168367 / % possible obs: 94.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 12.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.062 / Net I/σ(I): 9.3
Reflection shellResolution: 1.02→1.06 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.666 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 14404 / CC1/2: 0.233 / Rrim(I) all: 2.047 / % possible all: 80.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→35.16 Å / SU ML: 0.1388 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2606
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1602 3896 2.32 %
Rwork0.1289 164038 -
obs0.1296 167934 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.73 Å2
Refinement stepCycle: LAST / Resolution: 1.02→35.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 10 284 1860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021786
X-RAY DIFFRACTIONf_angle_d1.58422432
X-RAY DIFFRACTIONf_chiral_restr0.1073235
X-RAY DIFFRACTIONf_plane_restr0.0175323
X-RAY DIFFRACTIONf_dihedral_angle_d14.5536660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.030.39211060.38484163X-RAY DIFFRACTION67.7
1.03-1.050.37271110.36854979X-RAY DIFFRACTION79.58
1.05-1.060.32391380.31765638X-RAY DIFFRACTION90.85
1.06-1.070.31881360.28165833X-RAY DIFFRACTION92.66
1.07-1.090.27541440.26235714X-RAY DIFFRACTION92.47
1.09-1.110.25551420.25255868X-RAY DIFFRACTION93.27
1.11-1.120.26471440.2255895X-RAY DIFFRACTION94.45
1.12-1.140.20091350.20915856X-RAY DIFFRACTION94.6
1.14-1.160.19681360.19435956X-RAY DIFFRACTION94.95
1.16-1.180.21921440.18095923X-RAY DIFFRACTION95.11
1.18-1.20.18081500.17325922X-RAY DIFFRACTION95.38
1.2-1.230.16641380.16685921X-RAY DIFFRACTION95.01
1.23-1.260.23321120.16125685X-RAY DIFFRACTION91
1.26-1.290.17851710.1435970X-RAY DIFFRACTION96.19
1.29-1.320.15721200.13576011X-RAY DIFFRACTION96.64
1.32-1.350.15931790.12276080X-RAY DIFFRACTION96.75
1.35-1.390.1541320.12246029X-RAY DIFFRACTION96.95
1.39-1.440.16251340.11156055X-RAY DIFFRACTION96.82
1.44-1.490.1521550.10646056X-RAY DIFFRACTION96.93
1.49-1.550.15851330.09366076X-RAY DIFFRACTION97.66
1.55-1.620.12581460.10286046X-RAY DIFFRACTION96.98
1.62-1.70.13761390.09765789X-RAY DIFFRACTION93.02
1.7-1.810.13551430.10625992X-RAY DIFFRACTION96.42
1.81-1.950.12181390.09336188X-RAY DIFFRACTION98.8
1.95-2.150.14561540.11486158X-RAY DIFFRACTION99.14
2.15-2.460.14551460.11436199X-RAY DIFFRACTION98.75
2.46-3.10.14671380.12756000X-RAY DIFFRACTION96.68
3.1-35.160.15511310.11876036X-RAY DIFFRACTION96.62

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