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- PDB-6tq0: Crystal structure of the human Arc N-lobe bound to repeat peptide... -

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Basic information

Entry
Database: PDB / ID: 6tq0
TitleCrystal structure of the human Arc N-lobe bound to repeat peptide 5 from GKAP
Components
  • Activity-regulated cytoskeleton-associated protein
  • repeat peptide 5 from GKAP
KeywordsPROTEIN BINDING / Arc / capsid homology / GKAP
Function / homology
Function and homology information


virus-like capsid / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / postsynaptic specialization / clathrin-coated vesicle membrane / endoderm development / regulation of dendritic spine morphogenesis / NGF-stimulated transcription / dendritic spine morphogenesis / regulation of cell morphogenesis ...virus-like capsid / vesicle-mediated intercellular transport / neuronal ribonucleoprotein granule / postsynaptic specialization / 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 / Neurexins and neuroligins / 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 / chemical synaptic transmission / molecular adaptor activity / dendritic spine / postsynaptic membrane / postsynaptic density / membrane raft / neuronal cell body / mRNA binding / protein-containing complex binding / glutamatergic synapse / structural molecule activity / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SAPAP family / : / Guanylate-kinase-associated protein (GKAP) protein / 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
Disks large-associated protein 1 / Activity-regulated cytoskeleton-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHallin, E.I. / Bramham, C.R. / Kursula, P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council249951 Norway
CitationJournal: Biochem Biophys Rep / Year: 2021
Title: Structural properties and peptide ligand binding of the capsid homology domains of human Arc.
Authors: Hallin, E.I. / Bramham, C.R. / Kursula, P.
History
DepositionDec 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation
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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activity-regulated cytoskeleton-associated protein
B: repeat peptide 5 from GKAP
C: Activity-regulated cytoskeleton-associated protein
D: repeat peptide 5 from GKAP
E: Activity-regulated cytoskeleton-associated protein
F: repeat peptide 5 from GKAP
G: Activity-regulated cytoskeleton-associated protein
H: repeat peptide 5 from GKAP
I: Activity-regulated cytoskeleton-associated protein
J: repeat peptide 5 from GKAP
K: Activity-regulated cytoskeleton-associated protein
L: repeat peptide 5 from GKAP
M: Activity-regulated cytoskeleton-associated protein
N: repeat peptide 5 from GKAP
O: Activity-regulated cytoskeleton-associated protein
P: repeat peptide 5 from GKAP


Theoretical massNumber of molelcules
Total (without water)78,90516
Polymers78,90516
Non-polymers00
Water75742
1
A: Activity-regulated cytoskeleton-associated protein
B: repeat peptide 5 from GKAP


Theoretical massNumber of molelcules
Total (without water)9,8632
Polymers9,8632
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-11 kcal/mol
Surface area5020 Å2
MethodPISA
2
C: Activity-regulated cytoskeleton-associated protein
D: repeat peptide 5 from GKAP


Theoretical massNumber of molelcules
Total (without water)9,8632
Polymers9,8632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-9 kcal/mol
Surface area4750 Å2
MethodPISA
3
E: Activity-regulated cytoskeleton-associated protein
F: repeat peptide 5 from GKAP


Theoretical massNumber of molelcules
Total (without water)9,8632
Polymers9,8632
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area4910 Å2
MethodPISA
4
G: Activity-regulated cytoskeleton-associated protein
H: repeat peptide 5 from GKAP


Theoretical massNumber of molelcules
Total (without water)9,8632
Polymers9,8632
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-8 kcal/mol
Surface area4890 Å2
MethodPISA
5
I: Activity-regulated cytoskeleton-associated protein
J: repeat peptide 5 from GKAP


Theoretical massNumber of molelcules
Total (without water)9,8632
Polymers9,8632
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-12 kcal/mol
Surface area4830 Å2
MethodPISA
6
K: Activity-regulated cytoskeleton-associated protein
L: repeat peptide 5 from GKAP


Theoretical massNumber of molelcules
Total (without water)9,8632
Polymers9,8632
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-8 kcal/mol
Surface area4800 Å2
MethodPISA
7
M: Activity-regulated cytoskeleton-associated protein
N: repeat peptide 5 from GKAP


Theoretical massNumber of molelcules
Total (without water)9,8632
Polymers9,8632
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-10 kcal/mol
Surface area4820 Å2
MethodPISA
8
O: Activity-regulated cytoskeleton-associated protein
P: repeat peptide 5 from GKAP


Theoretical massNumber of molelcules
Total (without water)9,8632
Polymers9,8632
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-10 kcal/mol
Surface area4630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.310, 192.300, 39.560
Angle α, β, γ (deg.)90.000, 94.800, 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: Protein
Activity-regulated cytoskeleton-associated protein / hArc / Activity-regulated gene 3.1 protein homolog / Arg3.1


Mass: 8863.826 Da / Num. of mol.: 8
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
#2: Protein/peptide
repeat peptide 5 from GKAP


Mass: 999.278 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14490*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.89 Å3/Da / Density % sol: 34.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 1.2 M sodium citrate

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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: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. obs: 41702 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 53.8 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.053 / Rsym value: 0.045 / Net I/σ(I): 13.8
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3069 / CC1/2: 0.4 / Rrim(I) all: 2.073 / Rsym value: 1.786 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6tno

6tno


Resolution: 1.95→100 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2629 1997 5 %
Rwork0.2209 --
obs0.2229 41626 98.2 %
Displacement parametersBiso mean: 65.89 Å2
Refinement stepCycle: LAST / Resolution: 1.95→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5090 0 0 42 5132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125250
X-RAY DIFFRACTIONf_angle_d0.75457039
X-RAY DIFFRACTIONf_chiral_restr0.0517627
X-RAY DIFFRACTIONf_plane_restr0.0061914
X-RAY DIFFRACTIONf_dihedral_angle_d18.88493038

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