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- PDB-1pk8: Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP -

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Basic information

Entry
Database: PDB / ID: 1pk8
TitleCrystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP
Componentsrat synapsin I
KeywordsMEMBRANE PROTEIN / ATP binding / ATP grasp / calcium (II) ion
Function / homology
Function and homology information


synaptic vesicle cycle / synaptic vesicle clustering / Serotonin Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / extrinsic component of synaptic vesicle membrane / synaptonemal complex / regulation of synaptic vesicle cycle / neurotransmitter secretion / presynaptic active zone / regulation of synaptic vesicle exocytosis ...synaptic vesicle cycle / synaptic vesicle clustering / Serotonin Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / extrinsic component of synaptic vesicle membrane / synaptonemal complex / regulation of synaptic vesicle cycle / neurotransmitter secretion / presynaptic active zone / regulation of synaptic vesicle exocytosis / neuron development / synapse organization / Schaffer collateral - CA1 synapse / terminal bouton / calcium-dependent protein binding / synaptic vesicle / synaptic vesicle membrane / presynapse / actin binding / cell body / cytoskeleton / postsynaptic density / axon / synapse / dendrite / protein kinase binding / Golgi apparatus / ATP binding / identical protein binding
Similarity search - Function
Synapsin / Synapsin, conserved site / Synapsin, phosphorylation site / Synapsin, pre-ATP-grasp domain / Synapsin, ATP-binding domain / Synapsin pre-ATP-grasp domain / Synapsin, ATP binding domain / Synapsin N-terminal domain / Synapsins signature 1. / Synapsins signature 2. ...Synapsin / Synapsin, conserved site / Synapsin, phosphorylation site / Synapsin, pre-ATP-grasp domain / Synapsin, ATP-binding domain / Synapsin pre-ATP-grasp domain / Synapsin, ATP binding domain / Synapsin N-terminal domain / Synapsins signature 1. / Synapsins signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Synapsin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBrautigam, C.A. / Chelliah, Y. / Deisenhofer, J.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Tetramerization and ATP binding by a protein comprising the A, B, and C domains of rat synapsin I.
Authors: Brautigam, C.A. / Chelliah, Y. / Deisenhofer, J.
#1: Journal: Embo J. / Year: 1998
Title: Synapsin I is structurally similar to ATP-utilizing enzymes
Authors: Esser, L. / Wang, C.R. / Hosaka, M. / Smagula, C.S. / Sudhof, T.C. / Deisenhofer, J.
History
DepositionJun 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rat synapsin I
B: rat synapsin I
C: rat synapsin I
D: rat synapsin I
E: rat synapsin I
F: rat synapsin I
G: rat synapsin I
H: rat synapsin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,81726
Polymers364,3158
Non-polymers4,50218
Water11,980665
1
A: rat synapsin I
B: rat synapsin I
C: rat synapsin I
D: rat synapsin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,47114
Polymers182,1584
Non-polymers2,31310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15690 Å2
ΔGint-108 kcal/mol
Surface area47280 Å2
MethodPISA
2
E: rat synapsin I
F: rat synapsin I
G: rat synapsin I
H: rat synapsin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,34712
Polymers182,1584
Non-polymers2,1898
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-116 kcal/mol
Surface area46240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.600, 78.400, 135.000
Angle α, β, γ (deg.)80.60, 76.90, 71.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
rat synapsin I


Mass: 45539.398 Da / Num. of mol.: 8 / Fragment: A, B & C domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: SYN1 / Plasmid: pSynABC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P09951
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Details: Sigma Chemical Corp.
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Details: Sigma Chemical Corp. / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O / Details: Sigma Chemical Corp.

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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: 1.89 Å3/Da / Density % sol: 34.82 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEGMME 5000, Tris, NaCl, Ca.ATP, EDTA, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlprotein1drop
210 mMcalcium ATP1drop
3150 mMTris1reservoirpH7.5
415-20 %(w/v)PEG5000 MME1reservoir
5300 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 17, 2000
RadiationMonochromator: Double crystal monochromator, Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 150398 / % possible obs: 96.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 19 Å2 / Rsym value: 0.058 / Net I/σ(I): 20.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 14381 / Rsym value: 0.373 / % possible all: 92
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 144586 / Num. measured all: 522852 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.373

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AUX, ATPgammaS and Ca2+ removed

1aux


Resolution: 2.1→20 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MODIFIED ENGH & HUBER
Details: Although the A, B, and C domains of rat Synapsin I were included in crystallization, only the C domain was observed. Some side chain atoms were set to an occupancy of 0.00 because of ...Details: Although the A, B, and C domains of rat Synapsin I were included in crystallization, only the C domain was observed. Some side chain atoms were set to an occupancy of 0.00 because of disorder. Two conformations of ATP were modeled and refined due to ample evidence in the electron density maps. The differing phosphate positions would probably necessitate a movement in the associated Ca2+ ions, but only one Ca2+ was modeled per pair of ATP conformations
RfactorNum. reflection% reflectionSelection details
Rfree0.259 14256 -random
Rwork0.222 ---
all0.235 149733 --
obs0.222 142899 91.9 %-
Solvent computationSolvent model: flat model / Bsol: 37.4817 Å2 / ksol: 0.341215 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.03 Å21.83 Å2-0.7 Å2
2--0.74 Å2-0.42 Å2
3----4.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18531 0 512 665 19708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.007
RfactorNum. reflection% reflection
Rfree0.34 2100 -
Rwork0.289 --
obs-19216 82.2 %
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.5

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