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- PDB-4wbe: Crystal structure of the HR-1 domain of human caprin-1 in the C12... -

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Basic information

Entry
Database: PDB / ID: 4wbe
TitleCrystal structure of the HR-1 domain of human caprin-1 in the C121 space group
ComponentsCaprin-1
KeywordsRNA BINDING PROTEIN / all alpha helical
Function / homology
Function and homology information


regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / positive regulation of stress granule assembly / non-membrane-bounded organelle assembly / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / intracellular non-membrane-bounded organelle / cell leading edge / signaling adaptor activity / molecular condensate scaffold activity / molecular function activator activity ...regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / positive regulation of stress granule assembly / non-membrane-bounded organelle assembly / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / intracellular non-membrane-bounded organelle / cell leading edge / signaling adaptor activity / molecular condensate scaffold activity / molecular function activator activity / P-body / cytoplasmic stress granule / lamellipodium / negative regulation of translation / cell differentiation / mRNA binding / dendrite / synapse / RNA binding / ATP binding / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWu, Y. / Zhu, J. / Huang, X. / Du, Z.
CitationJournal: To be published
Title: Crystal structure of the HR-1 domain of human caprin-1 in the C121 space group
Authors: Wu, Y. / Zhu, J. / Huang, X. / Du, Z.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 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_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caprin-1
B: Caprin-1
C: Caprin-1


Theoretical massNumber of molelcules
Total (without water)42,7383
Polymers42,7383
Non-polymers00
Water4,846269
1
A: Caprin-1

A: Caprin-1


Theoretical massNumber of molelcules
Total (without water)28,4922
Polymers28,4922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3340 Å2
ΔGint-16 kcal/mol
Surface area13740 Å2
MethodPISA
2
B: Caprin-1
C: Caprin-1


Theoretical massNumber of molelcules
Total (without water)28,4922
Polymers28,4922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-19 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.950, 77.460, 58.020
Angle α, β, γ (deg.)90.000, 90.300, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASN / End label comp-ID: ASN

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain AAA132 - 2511 - 120
2chain BBB132 - 2511 - 120
3chain CCC133 - 2512 - 120
Detailsbiological unit is the same as asym.

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Components

#1: Protein Caprin-1 / / Cell cycle-associated protein 1 / Cytoplasmic activation- and proliferation-associated protein 1 / ...Cell cycle-associated protein 1 / Cytoplasmic activation- and proliferation-associated protein 1 / GPI-anchored membrane protein 1 / GPI-anchored protein p137 / p137GPI / Membrane component chromosome 11 surface marker 1 / RNA granule protein 105


Mass: 14246.061 Da / Num. of mol.: 3 / Fragment: unp residues 132-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPRIN1, GPIAP1, GPIP137, M11S1, RNG105 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14444
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% PEG750MME, 0.1 M Tris, 0.1 M potassium fluoride, 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: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→32.38 Å / Num. obs: 29462 / % possible obs: 98.9 % / Redundancy: 4.2 % / Net I/σ(I): 5.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→32.384 Å / FOM work R set: 0.847 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 1912 6.85 %
Rwork0.1962 25981 -
obs0.1986 27893 93.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.77 Å2 / Biso mean: 37.96 Å2 / Biso min: 9.31 Å2
Refinement stepCycle: final / Resolution: 2.05→32.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 0 269 3258
Biso mean---38.62 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053034
X-RAY DIFFRACTIONf_angle_d0.9424084
X-RAY DIFFRACTIONf_chiral_restr0.067452
X-RAY DIFFRACTIONf_plane_restr0.004532
X-RAY DIFFRACTIONf_dihedral_angle_d13.8321191
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1770X-RAY DIFFRACTION11.352TORSIONAL
12B1770X-RAY DIFFRACTION11.352TORSIONAL
13C1770X-RAY DIFFRACTION11.352TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10130.30021240.28321645176985
2.1013-2.15810.24671260.25771740186687
2.1581-2.22160.26421250.24351741186689
2.2216-2.29320.27211350.23131771190690
2.2932-2.37520.25671340.21421798193291
2.3752-2.47030.23681350.2141833196893
2.4703-2.58260.25381310.21091913204495
2.5826-2.71870.22831410.19931886202796
2.7187-2.8890.23981400.2161936207697
2.889-3.11190.2621430.20151928207197
3.1119-3.42470.24171400.19261938207897
3.4247-3.91950.20761470.17061945209298
3.9195-4.93540.20161440.1571951209598
4.9354-32.38840.21541470.19421956210396
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2777-0.67710.19192.77770.38411.8146-0.265-0.0590.01040.05250.26180.2069-0.02380.07640.05950.03690.007-0.03360.0563-0.01980.1488-6.541117.650923.3176
22.0518-1.07480.13271.0047-0.53212.43890.11480.4303-0.2108-0.3051-0.1194-0.03020.20090.0275-0.02130.150.01190.00230.179-0.04410.12484.699713.149619.2073
32.86790.1893-0.1033.8681-0.28692.18670.27710.6353-0.1244-1.2595-0.04191.6188-0.06760.00620.61310.08170.00050.10960.2747-0.0649-0.4142-4.852216.21614.0153
42.2531.2035-0.42912.6142-1.12311.57880.0798-0.13670.181-0.0369-0.1159-0.017-0.07140.00840.01730.1946-0.0718-0.0050.14140.01030.3028-25.69015.219233.0597
51.5571-0.3514-0.23261.6018-0.71882.3294-0.33390.62550.1306-0.580.33760.1058-0.1088-0.55940.04770.4226-0.1326-0.11560.35050.11070.282-34.85554.177120.4839
62.87731.8229-1.78511.5312-0.87991.6958-0.1538-0.0005-0.2327-0.2068-0.0714-0.22580.25610.08840.11550.1764-0.0447-0.02660.1398-0.020.2755-32.8319-10.660535.8299
73.04951.2846-0.12793.7031-0.47053.2523-0.10460.34990.121-0.99740.1956-0.35220.11230.16050.08870.266-0.05850.02670.21940.02320.2176-27.2724.329623.4958
84.3041-0.0958-0.00463.97150.27132.41360.0352-0.0598-0.8801-0.1759-0.0738-0.47610.13540.4025-0.02050.284-0.0728-0.06130.17890.01870.3902-24.9213-7.713441.5356
93.03030.5475-1.77941.11540.27072.1188-0.5077-0.25050.1451-0.2288-0.34030.86630.3591-0.7265-0.88810.5228-0.06690.36670.5476-0.110.7233-45.795-2.978254.5933
101.44320.9812-1.36250.7187-1.02341.47980.0185-0.40150.32780.19210.02910.39480.2319-0.3566-0.35860.601-0.22570.17570.6320.03270.3894-41.9997-9.760461.4681
112.0013-0.1490.51831.22-0.22653.0547-0.3901-0.49450.69860.9367-0.35890.6933-1.0204-0.0224-0.55730.5971-0.06920.19170.388-0.28540.284-34.20454.311254.2598
121.1994-0.2962-0.32062.6357-1.30182.36690.1935-0.75220.3470.4935-0.1986-0.0575-0.8640.80240.07230.4496-0.22010.0110.2365-0.09740.263-25.55429.54941.7239
132.30640.63130.39451.45920.7660.4961-0.042-1.1809-0.21580.4838-0.0633-0.08330.03770.4693-0.05550.5265-0.1869-0.03610.5451-0.03930.1402-25.7164-1.913455.8953
141.213-0.0904-1.51095.74422.02423.6704-0.01310.2057-0.1928-0.2295-0.01960.595-0.156-0.6688-0.25030.3735-0.17020.01740.38230.05580.2022-42.513-11.555948.2094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 132 through 170 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 219 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 220 through 251 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 132 through 170 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 171 through 193 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 194 through 218 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 219 through 251 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 133 through 160 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 161 through 169 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 170 through 179 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 180 through 193 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 194 through 219 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 220 through 242 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 243 through 251 )C0

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