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- PDB-4oum: Crystal structure of human Caprin-2 C1q domain -

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Basic information

Entry
Database: PDB / ID: 4oum
TitleCrystal structure of human Caprin-2 C1q domain
ComponentsCaprin-2Aspirin
KeywordsSIGNALING PROTEIN / C1q domain / Wnt signaling
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 / negative regulation of translation / receptor complex / 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 / negative regulation of translation / receptor complex / signaling receptor binding / centrosome / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / nucleoplasm / metal ion binding / plasma membrane / cytosol / cytoplasm
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. / Jelly Rolls - #40 ...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. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / ISOPROPYL ALCOHOL / Caprin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.491 Å
AuthorsSong, X. / Li, L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural insights into the C1q domain of Caprin-2 in canonical Wnt signaling
Authors: Miao, H. / Jia, Y. / Xie, S. / Wang, X. / Zhao, J. / Chu, Y. / Zhou, Z. / Shi, Z. / Song, X. / Li, L.
History
DepositionFeb 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caprin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3906
Polymers15,8261
Non-polymers5645
Water1,47782
1
A: Caprin-2
hetero molecules

A: Caprin-2
hetero molecules

A: Caprin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,16918
Polymers47,4783
Non-polymers1,69115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7680 Å2
ΔGint-17 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.499, 77.499, 53.451
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1374-

HOH

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Components

#1: Protein Caprin-2 / Aspirin / 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: 15825.954 Da / Num. of mol.: 1 / Fragment: UNP residues 996-1127 / Mutation: D1078A, E1084A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1QDC1, CAPRIN2, EEG1, KIAA1873, RNG140 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q6IMN6
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.95 Å3/Da / Density % sol: 36.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: 100mM sodium citrate pH5.6, 12% 2-propanol, 11% PEG4000, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. all: 19557 / Num. obs: 19420 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Net I/σ(I): 29.3
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 9.2 / Num. unique all: 984 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1O91

1o91


Resolution: 1.491→22.372 Å / SU ML: 0.14 / σ(F): 2.04 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 1932 9.95 %RANDOM
Rwork0.1861 ---
obs0.1891 19419 99.35 %-
all-19546 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.491→22.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 38 82 1159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061158
X-RAY DIFFRACTIONf_angle_d1.1591567
X-RAY DIFFRACTIONf_dihedral_angle_d20.868420
X-RAY DIFFRACTIONf_chiral_restr0.08171
X-RAY DIFFRACTIONf_plane_restr0.005201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.491-1.52790.24021380.20911252100
1.5279-1.56920.23661420.20081257100
1.5692-1.61540.22821350.2021262100
1.6154-1.66750.24351400.18981255100
1.6675-1.72710.24371420.19841268100
1.7271-1.79620.23711380.19361247100
1.7962-1.87790.24781400.19381246100
1.8779-1.97690.21181460.18771268100
1.9769-2.10070.21491400.1921264100
2.1007-2.26270.20141360.19491230100
2.2627-2.49020.23331380.19871277100
2.4902-2.84990.23741350.19541264100
2.8499-3.58810.19181390.1726123699
3.5881-22.37450.20411230.1721116192

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