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- PDB-5j97: Dimerization domain of cytoplasmic activation/proliferation-assoc... -

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Basic information

Entry
Database: PDB / ID: 5j97
TitleDimerization domain of cytoplasmic activation/proliferation-associated protein-2 (caprin-2)
ComponentsCaprin-2Aspirin
KeywordsRNA BINDING PROTEIN / all alpha helical
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 / negative regulation of translation / cell differentiation / 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 / negative regulation of translation / cell differentiation / 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. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsWu, Y. / Zhu, J. / Huang, X. / Du, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Dimerization domain of cytoplasmic activation/proliferation-associated protein-2 (caprin-2)
Authors: Du, Z. / Wu, Y. / Zhu, J. / Huang, X.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,6322
Polymers31,6322
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-20 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.020, 71.020, 133.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B

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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: 15815.776 Da / Num. of mol.: 2 / Fragment: UNP residues 199-329
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) / Strain (production host): BL21(DE3) / References: UniProt: Q6IMN6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG8000, 0.1 M Tris (pH8.0), 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.55→40.158 Å / Num. obs: 11231 / % possible obs: 96.6 % / Redundancy: 10.4 % / Net I/σ(I): 19.5
Reflection shellHighest resolution: 2.55 Å

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALAdata scaling
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→40.16 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.76
RfactorNum. reflection% reflection
Rfree0.244 1094 9.97 %
Rwork0.211 --
obs0.214 10974 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.81 Å2
Refinement stepCycle: LAST / Resolution: 2.55→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 0 77 2090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052050
X-RAY DIFFRACTIONf_angle_d0.992758
X-RAY DIFFRACTIONf_dihedral_angle_d16.787794
X-RAY DIFFRACTIONf_chiral_restr0.077307
X-RAY DIFFRACTIONf_plane_restr0.005348
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A1129X-RAY DIFFRACTIONPOSITIONAL
12B1129X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5502-2.66620.32821270.27831137X-RAY DIFFRACTION88
2.6662-2.80670.35071260.26661166X-RAY DIFFRACTION90
2.8067-2.98250.29151300.25131192X-RAY DIFFRACTION92
2.9825-3.21270.32611370.25151216X-RAY DIFFRACTION94
3.2127-3.53590.29871370.22221247X-RAY DIFFRACTION95
3.5359-4.04710.23761380.19031252X-RAY DIFFRACTION96
4.0471-5.09730.19571460.17591300X-RAY DIFFRACTION96
5.0973-40.1630.19531530.20151370X-RAY DIFFRACTION95

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