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- PDB-8k9c: Structure of human Caprin-2 HR1 domain -

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Basic information

Entry
Database: PDB / ID: 8k9c
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 / cell differentiation / receptor complex / 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 / cell differentiation / receptor complex / 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: 2.32 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
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caprin-2
B: Caprin-2


Theoretical massNumber of molelcules
Total (without water)58,8202
Polymers58,8202
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-40 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.721, 65.322, 112.203
Angle α, β, γ (deg.)90.00, 113.75, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: 29410.104 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.87 Å3/Da / Density % sol: 74.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 12-15% PEG3350, 20 mM lithiuym chloride

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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: 2.32→50 Å / Num. obs: 75003 / % possible obs: 97.6 % / Redundancy: 6 % / Biso Wilson estimate: 56.29 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 31.67
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 1885

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.32→30.21 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 3855 5.14 %
Rwork0.2176 --
obs0.2188 74950 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→30.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 0 83 3390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.639
X-RAY DIFFRACTIONf_dihedral_angle_d4.143442
X-RAY DIFFRACTIONf_chiral_restr0.036510
X-RAY DIFFRACTIONf_plane_restr0.005582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.350.3234630.31111247X-RAY DIFFRACTION47
2.35-2.380.34031360.3182515X-RAY DIFFRACTION96
2.38-2.410.35141480.31492724X-RAY DIFFRACTION96
2.41-2.440.29521300.28552478X-RAY DIFFRACTION96
2.44-2.480.33551380.27882513X-RAY DIFFRACTION97
2.48-2.510.32311440.29012659X-RAY DIFFRACTION97
2.51-2.550.3311430.27152574X-RAY DIFFRACTION97
2.55-2.590.38551380.2832579X-RAY DIFFRACTION97
2.59-2.640.27521390.28152604X-RAY DIFFRACTION97
2.64-2.690.33821370.27772608X-RAY DIFFRACTION97
2.69-2.740.30281450.26972620X-RAY DIFFRACTION98
2.74-2.790.27391390.2642569X-RAY DIFFRACTION97
2.79-2.850.32231460.27442665X-RAY DIFFRACTION98
2.85-2.920.28561350.25732510X-RAY DIFFRACTION98
2.92-2.990.31121410.26252672X-RAY DIFFRACTION98
2.99-3.070.30881430.25022629X-RAY DIFFRACTION98
3.07-3.160.28231430.26392578X-RAY DIFFRACTION97
3.16-3.270.30141450.24892610X-RAY DIFFRACTION98
3.27-3.380.2771390.23942593X-RAY DIFFRACTION98
3.38-3.520.22841440.22062646X-RAY DIFFRACTION98
3.52-3.680.22721430.21962635X-RAY DIFFRACTION98
3.68-3.870.22891410.2032614X-RAY DIFFRACTION98
3.87-4.110.23031380.19192588X-RAY DIFFRACTION98
4.11-4.430.21471450.1782597X-RAY DIFFRACTION97
4.43-4.870.21691400.18352554X-RAY DIFFRACTION96
4.87-5.580.22041450.20182614X-RAY DIFFRACTION98
5.58-7.010.19451400.21052626X-RAY DIFFRACTION98
7.01-30.210.16111270.16232274X-RAY DIFFRACTION86

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