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- PDB-7r24: Crystal structure of rat Arc CTD in complex with two anti-Arc nan... -

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Basic information

Entry
Database: PDB / ID: 7r24
TitleCrystal structure of rat Arc CTD in complex with two anti-Arc nanobodies
Components
  • (anti-Arc nanobody) x 2
  • Activity-regulated cytoskeleton-associated protein
KeywordsSTRUCTURAL PROTEIN / capsid / nanobody / Gag homology
Function / homology
Function and homology information


postsynaptic endosome / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / response to morphine / regulation of cell morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / regulation of long-term synaptic potentiation ...postsynaptic endosome / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / response to morphine / regulation of cell morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / regulation of long-term synaptic potentiation / positive regulation of AMPA receptor activity / 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 / postsynaptic density membrane / modulation of chemical synaptic transmission / protein homooligomerization / endocytosis / extracellular vesicle / cell migration / actin cytoskeleton / cell cortex / early endosome membrane / dendritic spine / membrane raft / mRNA binding / glutamatergic synapse / dendrite / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Activity-regulated cytoskeleton-associated protein, capsid domain / Activity-regulated cytoskeleton-associated protein, N-terminal domain / Arc MA domain / Activity-regulated cytoskeleton-associated protein / Activity-regulated cytoskeleton-associated protein, C-terminal domain / Arc C-lobe
Similarity search - Domain/homology
Activity-regulated cytoskeleton-associated protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMarkusson, S. / Kursula, P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council249951 Norway
CitationJournal: To Be Published
Title: Crystal structure of rat Arc CTD in complex with two anti-Arc nanobodies
Authors: Markusson, S. / Kursula, P.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activity-regulated cytoskeleton-associated protein
C: anti-Arc nanobody
E: anti-Arc nanobody


Theoretical massNumber of molelcules
Total (without water)72,2623
Polymers72,2623
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-11 kcal/mol
Surface area19260 Å2
Unit cell
Length a, b, c (Å)40.880, 92.810, 114.650
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

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Components

#1: Protein Activity-regulated cytoskeleton-associated protein / / Activity-regulated gene 3.1 protein / ARC/ARG3.1 / Arg3.1


Mass: 45055.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arc / Production host: Escherichia coli (E. coli) / References: UniProt: Q63053
#2: Antibody anti-Arc nanobody


Mass: 13127.566 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)
#3: Antibody anti-Arc nanobody


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)

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG10000, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 22999 / % possible obs: 99.2 % / Redundancy: 7.5 % / Biso Wilson estimate: 48.65 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.293 / Net I/σ(I): 6.7
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 885 / CC1/2: 0.478 / Rrim(I) all: 2.552 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X3H,4X3X,6H16,4FHB

4x3h

4x3x

6h16

4fhb


Resolution: 2.7→38.51 Å / SU ML: 0.4679 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.331
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2739 2278 9.93 %
Rwork0.2568 20654 -
obs0.2585 22932 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.82 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 0 0 3168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243240
X-RAY DIFFRACTIONf_angle_d0.5274380
X-RAY DIFFRACTIONf_chiral_restr0.0391454
X-RAY DIFFRACTIONf_plane_restr0.0045567
X-RAY DIFFRACTIONf_dihedral_angle_d18.43451194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.38071340.40751252X-RAY DIFFRACTION95.98
2.76-2.820.42491420.36821276X-RAY DIFFRACTION99.79
2.82-2.890.34361480.3531338X-RAY DIFFRACTION99.2
2.89-2.970.40851380.35781240X-RAY DIFFRACTION98.29
2.97-3.060.32591460.34091305X-RAY DIFFRACTION99.66
3.06-3.160.44221410.33241290X-RAY DIFFRACTION99.03
3.16-3.270.32981420.32691294X-RAY DIFFRACTION99.72
3.27-3.40.31821400.28721297X-RAY DIFFRACTION99.17
3.4-3.560.30191360.29751283X-RAY DIFFRACTION99.65
3.56-3.740.21891470.26211335X-RAY DIFFRACTION99.73
3.74-3.980.27181440.24071259X-RAY DIFFRACTION99.57
3.98-4.280.21831470.20341297X-RAY DIFFRACTION99.52
4.29-4.720.18731460.19541302X-RAY DIFFRACTION99.86
4.72-5.40.23851340.20661308X-RAY DIFFRACTION99.86
5.4-6.790.27631490.23331314X-RAY DIFFRACTION99.66
6.8-38.510.2021440.19041264X-RAY DIFFRACTION97.91

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