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- PDB-4ous: Crystal structure of zebrafish Caprin-2 C1q domain -

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Basic information

Entry
Database: PDB / ID: 4ous
TitleCrystal structure of zebrafish Caprin-2 C1q domain
ComponentsCaprin-2
KeywordsSIGNALING PROTEIN / C1q domain / Wnt signaling
Function / homology
Function and homology information


: / positive regulation of dendritic spine morphogenesis / dorsal/ventral pattern formation / regulation of growth / positive regulation of dendrite morphogenesis / positive regulation of Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / negative regulation of translation / RNA binding / metal ion binding ...: / positive regulation of dendritic spine morphogenesis / dorsal/ventral pattern formation / regulation of growth / positive regulation of dendrite morphogenesis / positive regulation of Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / negative regulation of translation / RNA binding / metal ion binding / plasma membrane / 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
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Caprin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1202
Polymers16,0801
Non-polymers401
Water2,342130
1
A: Caprin-2
hetero molecules

A: Caprin-2
hetero molecules

A: Caprin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3616
Polymers48,2403
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6550 Å2
ΔGint-46 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.985, 94.985, 94.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1201-

CA

21A-1396-

HOH

31A-1400-

HOH

41A-1401-

HOH

51A-1402-

HOH

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Components

#1: Protein Caprin-2 / RNA granule protein 140


Mass: 16080.109 Da / Num. of mol.: 1 / Fragment: UNP residues 780-914 / Mutation: M998L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: caprin2, rng140, si:ch211-11c20.4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q5RJ80
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 4.0M sodium nitrate, 0.1M Bis-Tris propane pH7.0, 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: RAYONIX MX-225 / Detector: CCD / Date: Jun 23, 2010
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: 1.05→50 Å / Num. all: 66333 / Num. obs: 63149 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Net I/σ(I): 17.9
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 6613 / % 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: 1O91

1o91


Resolution: 1.05→10.62 Å / SU ML: 0.06 / σ(F): 0.01 / Phase error: 12.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1613 2002 3.49 %RANDOM
Rwork0.152 ---
obs0.1523 57340 86.69 %-
all-66144 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→10.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 1 130 1166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051100
X-RAY DIFFRACTIONf_angle_d1.1271506
X-RAY DIFFRACTIONf_dihedral_angle_d12.418384
X-RAY DIFFRACTIONf_chiral_restr0.048165
X-RAY DIFFRACTIONf_plane_restr0.006196
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 (%)
1.0501-1.07630.19281320.1821389186
1.0763-1.10540.15871390.1595392687
1.1054-1.13790.14661430.1457405190
1.1379-1.17460.14941530.1384412791
1.1746-1.21650.16671490.1413407090
1.2165-1.26510.13591530.1479411091
1.2651-1.32260.16791510.1503407990
1.3226-1.39220.15861530.1436415292
1.3922-1.47920.15121430.1481419392
1.4792-1.59310.14731540.1375423993
1.5931-1.75270.16381570.1415426894
1.7527-2.00490.16121270.1519338774
2.0049-2.52030.13711130.1547343475
2.5203-10.62020.18881350.1653341173
Refinement TLS params.Method: refined / Origin x: -33.1006 Å / Origin y: -20.2713 Å / Origin z: -15.6584 Å
111213212223313233
T0.0492 Å2-0.0015 Å20.0031 Å2-0.0476 Å2-0.0024 Å2--0.0484 Å2
L0.496 °2-0.0311 °2-0.0033 °2-0.3845 °2-0.0986 °2--0.501 °2
S-0.0009 Å °-0.0198 Å °-0.0034 Å °0.0445 Å °-0.0047 Å °0.0442 Å °-0.0317 Å °-0.0315 Å °0 Å °
Refinement TLS groupSelection details: all

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