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- PDB-7r1z: C-terminal domain of hArc in complex with nanobodies H11 and C11,... -

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Basic information

Entry
Database: PDB / ID: 7r1z
TitleC-terminal domain of hArc in complex with nanobodies H11 and C11, collapsed crystal form
Components
  • Activity-regulated cytoskeleton-associated protein
  • NbArc-C11
  • NbArc-H11
KeywordsSIGNALING PROTEIN / Arc / Nanobody / Signaling / Plasticity
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 / NGF-stimulated transcription / dendritic spine morphogenesis / regulation of cell morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization ...postsynaptic endosome / 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 / 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 / dendritic spine / membrane raft / mRNA binding / neuronal cell body / glutamatergic synapse / 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 speciesVicugna pacos (alpaca)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMarkusson, S. / Kursula, P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway249951 Norway
CitationJournal: Plos One / Year: 2022
Title: High-affinity anti-Arc nanobodies provide tools for structural and functional studies.
Authors: Markusson, S. / Hallin, E.I. / Bustad, H.J. / Raasakka, A. / Xu, J. / Muruganandam, G. / Loris, R. / Martinez, A. / Bramham, C.R. / Kursula, P.
History
DepositionFeb 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 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
E: NbArc-H11
A: Activity-regulated cytoskeleton-associated protein
C: NbArc-C11


Theoretical massNumber of molelcules
Total (without water)48,9503
Polymers48,9503
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-11 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.260, 139.290, 43.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Antibody NbArc-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 BL21(DE3) (bacteria)
#2: Protein Activity-regulated cytoskeleton-associated protein / / hArc / Activity-regulated gene 3.1 protein homolog / ARC/ARG3.1 / Arg3.1


Mass: 21743.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: ARC, KIAA0278 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q7LC44
#3: Antibody NbArc-C11


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 BL21(DE3) (bacteria)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 17% PEG3350. Produced from seed crystals grown in 12% PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.94→48 Å / Num. obs: 26403 / % possible obs: 0.865 % / Redundancy: 11.9 % / Biso Wilson estimate: 34.95 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.13 / Net I/σ(I): 13.13
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 6.72 % / Mean I/σ(I) obs: 0.83 / Num. unique obs: 1025 / CC1/2: 0.351 / Rrim(I) all: 2.356 / % possible all: 46.2

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Processing

Software
NameVersionClassification
PHENIXdev_3958refinement
XDSFeb 5, 2021data reduction
XSCALEFeb 5, 2021data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TNP

6tnp


Resolution: 1.94→48 Å / SU ML: 0.268 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2425 1999 7.57 %
Rwork0.197 24398 -
obs0.2005 26397 86.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.84 Å2
Refinement stepCycle: LAST / Resolution: 1.94→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 0 163 3071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333000
X-RAY DIFFRACTIONf_angle_d0.60774061
X-RAY DIFFRACTIONf_chiral_restr0.0419419
X-RAY DIFFRACTIONf_plane_restr0.0042526
X-RAY DIFFRACTIONf_dihedral_angle_d14.91191099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.4107740.3408917X-RAY DIFFRACTION46.29
1.99-2.040.3484860.26961055X-RAY DIFFRACTION53.69
2.04-2.10.34831000.23571215X-RAY DIFFRACTION61.59
2.1-2.170.32611150.22181400X-RAY DIFFRACTION69.88
2.17-2.250.28821340.21561637X-RAY DIFFRACTION83.22
2.25-2.340.28061570.22261907X-RAY DIFFRACTION95.91
2.34-2.440.31061630.22391998X-RAY DIFFRACTION99.86
2.44-2.570.29361650.21722004X-RAY DIFFRACTION99.86
2.57-2.730.25781640.20682003X-RAY DIFFRACTION99.95
2.73-2.950.24351620.21851979X-RAY DIFFRACTION99.07
2.95-3.240.25611660.21962022X-RAY DIFFRACTION99.86
3.24-3.710.24741660.18412039X-RAY DIFFRACTION99.86
3.71-4.670.19641690.16042053X-RAY DIFFRACTION99.15
4.68-480.20361780.18562169X-RAY DIFFRACTION99.45

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