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- PDB-8k9d: Structure of human Caprin-2 HR1 domain -

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Basic information

Entry
Database: PDB / ID: 8k9d
TitleStructure of human Caprin-2 HR1 domain
ComponentsCaprin-2
KeywordsSIGNALING PROTEIN / Wnt signaling / homodimer
Function / homology
Function and homology information


dorsal/ventral axis specification / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / negative regulation of cell growth / positive regulation of canonical Wnt signaling pathway / receptor complex / cell differentiation / negative regulation of translation / signaling receptor binding / centrosome ...dorsal/ventral axis specification / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / negative regulation of cell growth / positive regulation of canonical Wnt signaling pathway / receptor complex / cell differentiation / negative regulation of translation / signaling receptor binding / centrosome / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / nucleoplasm / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Cytoplasmic activation/proliferation-associated protein-1 C term / Cytoplasmic activation/proliferation-associated protein-1 C term / Caprin / Caprin-1 dimerization domain / Caprin-1 dimerization domain / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsSong, X.M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31530094 China
National Natural Science Foundation of China (NSFC)31100532 China
CitationJournal: To Be Published
Title: Structural insights into the Caprin-2 HR1 domain in canonical Wnt signaling
Authors: Song, X.M.
History
DepositionJul 31, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caprin-2


Theoretical massNumber of molelcules
Total (without water)30,5481
Polymers30,5481
Non-polymers00
Water00
1
A: Caprin-2

A: Caprin-2


Theoretical massNumber of molelcules
Total (without water)61,0962
Polymers61,0962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2060 Å2
ΔGint-17 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.852, 281.903, 63.449
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Caprin-2 / C1q domain-containing protein 1 / Cytoplasmic activation/proliferation-associated protein 2 / ...C1q domain-containing protein 1 / Cytoplasmic activation/proliferation-associated protein 2 / Gastric cancer multidrug resistance-associated protein / Protein EEG-1 / RNA granule protein 140


Mass: 30547.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPRIN2, C1QDC1, EEG1, KIAA1873, RNG140 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IMN6
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: 4.19 Å3/Da / Density % sol: 70.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 20-25% PEG3350, 1.6M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 3.11→50 Å / Num. obs: 14540 / % possible obs: 96.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 17.3
Reflection shellResolution: 3.11→3.66 Å / Rmerge(I) obs: 0.782 / Num. unique obs: 408

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 3.3→35.24 Å / SU ML: 0.525 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.5508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3022 1457 10.02 %
Rwork0.2895 13083 -
obs0.2907 14540 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 0 0 931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027947
X-RAY DIFFRACTIONf_angle_d0.57581281
X-RAY DIFFRACTIONf_chiral_restr0.0361146
X-RAY DIFFRACTIONf_plane_restr0.0038164
X-RAY DIFFRACTIONf_dihedral_angle_d4.5995129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.420.48421360.41091200X-RAY DIFFRACTION89.6
3.42-3.560.4211480.36441344X-RAY DIFFRACTION99.2
3.56-3.720.47071390.41351308X-RAY DIFFRACTION98.5
3.72-3.910.36761480.32981322X-RAY DIFFRACTION99.39
3.91-4.160.3621500.28671310X-RAY DIFFRACTION99.79
4.16-4.480.23241490.23661354X-RAY DIFFRACTION99.8
4.48-4.930.26361470.25611315X-RAY DIFFRACTION99.66
4.93-5.640.29521490.31741334X-RAY DIFFRACTION99.4
5.64-7.090.33861510.34751329X-RAY DIFFRACTION99.8
7.1-35.240.25021400.23751267X-RAY DIFFRACTION94.88

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