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- PDB-7vs3: The crystal structure of rat calcium-dependent activator protein ... -

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Basic information

Entry
Database: PDB / ID: 7vs3
TitleThe crystal structure of rat calcium-dependent activator protein for secretion (CAPS) C2PH
ComponentsCalcium-dependent secretion activator 1
KeywordsEXOCYTOSIS / Ca2+-dependent exocytosis / Vesicle priming / Munc13 / CAPS / SNARE complex assembly
Function / homology
Function and homology information


extrinsic component of neuronal dense core vesicle membrane / catecholamine secretion / dense core granule / regulated exocytosis / presynaptic dense core vesicle exocytosis / vesicle organization / positive regulation of calcium ion-dependent exocytosis / synaptic vesicle priming / exocytosis / positive regulation of exocytosis ...extrinsic component of neuronal dense core vesicle membrane / catecholamine secretion / dense core granule / regulated exocytosis / presynaptic dense core vesicle exocytosis / vesicle organization / positive regulation of calcium ion-dependent exocytosis / synaptic vesicle priming / exocytosis / positive regulation of exocytosis / phosphatidylinositol-4,5-bisphosphate binding / establishment of localization in cell / protein transport / presynapse / cytoplasmic vesicle / glutamatergic synapse / calcium ion binding / protein kinase binding
Similarity search - Function
Calcium-dependent secretion activator / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Domain of Unknown Function (DUF1041) / C2 domain / C2 domain profile. / PH domain / PH domain profile. ...Calcium-dependent secretion activator / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Domain of Unknown Function (DUF1041) / C2 domain / C2 domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Calcium-dependent secretion activator 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.595 Å
AuthorsZhou, H. / Wei, Z.Q. / Zhang, L. / Ren, Y.J. / Ma, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670846 China
National Natural Science Foundation of China (NSFC)31721002 China
CitationJournal: Structure / Year: 2023
Title: The C 2 and PH domains of CAPS constitute an effective PI(4,5)P2-binding unit essential for Ca 2+ -regulated exocytosis.
Authors: Zhang, L. / Li, L. / Wei, Z. / Zhou, H. / Liu, H. / Wang, S. / Ren, Y. / Dai, T. / Wang, J. / Hu, Z. / Ma, C.
History
DepositionOct 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-dependent secretion activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9744
Polymers27,6861
Non-polymers2883
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.940, 62.452, 64.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-802-

HOH

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Components

#1: Protein Calcium-dependent secretion activator 1 / Calcium-dependent activator protein for secretion 1 / CAPS-1 / rCAPS


Mass: 27685.623 Da / Num. of mol.: 1 / Fragment: C2PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cadps, Caps, Caps1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q62717
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.1M Tris pH 8.5, 2.5M ammonium sulfate / PH range: 8.0 - 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 7469 / % possible obs: 99 % / Redundancy: 9 % / Rrim(I) all: 0.225 / Net I/σ(I): 11.1
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 3 / Num. unique obs: 716 / Rrim(I) all: 0.779 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WI1, 3W56

1wi1

3w56


Resolution: 2.595→42.561 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 375 5.08 %
Rwork0.223 7013 -
obs0.2261 7388 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.3 Å2 / Biso mean: 40.8747 Å2 / Biso min: 30.21 Å2
Refinement stepCycle: final / Resolution: 2.595→42.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 15 22 1860
Biso mean--53.81 40.55 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031880
X-RAY DIFFRACTIONf_angle_d0.6132557
X-RAY DIFFRACTIONf_chiral_restr0.043282
X-RAY DIFFRACTIONf_plane_restr0.004325
X-RAY DIFFRACTIONf_dihedral_angle_d15.1621118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5952-2.97060.34911150.2823227198
2.9706-3.74240.28591270.22672320100
3.7424-42.5610.25531330.2028242299

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