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- PDB-4x3x: The crystal structure of Arc C-lobe -

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Basic information

Entry
Database: PDB / ID: 4x3x
TitleThe crystal structure of Arc C-lobe
ComponentsActivity-regulated cytoskeleton-associated protein
KeywordsSIGNALING PROTEIN / ENDOCYTOSIS MEDIATOR
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 / regulation of cell morphogenesis / response to morphine / 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 / regulation of cell morphogenesis / response to morphine / 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 / response to ethanol / dendritic spine / membrane raft / mRNA binding / glutamatergic synapse / dendrite / plasma membrane / cytoplasm / cytosol
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, W. / Ward, M. / Leahy, D. / Worley, P.
CitationJournal: Neuron / Year: 2015
Title: Structural basis of arc binding to synaptic proteins: implications for cognitive disease.
Authors: Zhang, W. / Wu, J. / Ward, M.D. / Yang, S. / Chuang, Y.A. / Xiao, M. / Li, R. / Leahy, D.J. / Worley, P.F.
History
DepositionDec 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activity-regulated cytoskeleton-associated protein


Theoretical massNumber of molelcules
Total (without water)10,6241
Polymers10,6241
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.067, 74.659, 38.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-409-

HOH

31A-414-

HOH

41A-415-

HOH

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Components

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


Mass: 10623.921 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 278-362
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 M SODIUM CITRATE, 0.1 M IMIDAZOLE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 13, 2013
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.9891
30.97951
ReflectionResolution: 2→50 Å / Num. obs: 11473 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.07 Å / % possible all: 90.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
RefinementMethod to determine structure: SAD / Resolution: 2→37.33 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1084 9.95 %
Rwork0.217 --
obs0.218 10895 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 0 22 720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019710
X-RAY DIFFRACTIONf_angle_d2.028956
X-RAY DIFFRACTIONf_dihedral_angle_d20.022285
X-RAY DIFFRACTIONf_chiral_restr0.134104
X-RAY DIFFRACTIONf_plane_restr0.01125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0018-2.09290.33161230.27271118X-RAY DIFFRACTION90
2.0929-2.20320.27591380.25811250X-RAY DIFFRACTION100
2.2032-2.34120.2561400.26081238X-RAY DIFFRACTION100
2.3412-2.52190.28811420.23141229X-RAY DIFFRACTION100
2.5219-2.77570.2161350.21821249X-RAY DIFFRACTION100
2.7757-3.17710.25071370.23721237X-RAY DIFFRACTION100
3.1771-4.00210.19851360.19261239X-RAY DIFFRACTION100
4.0021-37.3360.20581330.19881251X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.1495 Å / Origin y: 11.7581 Å / Origin z: -4.4532 Å
111213212223313233
T0.2457 Å2-0.0052 Å20.0245 Å2-0.246 Å20.0197 Å2--0.2571 Å2
L0.0296 °20.0289 °20.0163 °2-0.0473 °20.0031 °2--0.0208 °2
S-0.0807 Å °0.0166 Å °-0.0722 Å °-0.0885 Å °-0.013 Å °-0.0974 Å °0.0399 Å °0.0621 Å °0 Å °
Refinement TLS groupSelection details: all

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