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- PDB-2p0a: The crystal structure of human synapsin III (SYN3) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2p0a
TitleThe crystal structure of human synapsin III (SYN3) in complex with AMPPNP
ComponentsSynapsin-3
KeywordsNEUROPEPTIDE / synapsin / neurotransmitter release / schizophrenia / vesicle transport / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Serotonin Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / neurotransmitter secretion / regulation of synaptic transmission, GABAergic / synaptic vesicle membrane / synaptic vesicle / postsynaptic density / ATP binding
Similarity search - Function
Synapsin-2/3 / Synapsin / Synapsin, conserved site / Synapsin, phosphorylation site / Synapsin, pre-ATP-grasp domain / Synapsin, ATP-binding domain / Synapsin, N-terminal domain / Synapsin, ATP binding domain / Synapsin N-terminal / Synapsins signature 1. ...Synapsin-2/3 / Synapsin / Synapsin, conserved site / Synapsin, phosphorylation site / Synapsin, pre-ATP-grasp domain / Synapsin, ATP-binding domain / Synapsin, N-terminal domain / Synapsin, ATP binding domain / Synapsin N-terminal / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Synapsin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTurnbull, A.P. / Phillips, C. / Pike, A.C.W. / Elkins, J.M. / Gileadi, C. / Salah, E. / Niesen, F.H. / Burgess, N. / Gileadi, O. / Gorrec, F. ...Turnbull, A.P. / Phillips, C. / Pike, A.C.W. / Elkins, J.M. / Gileadi, C. / Salah, E. / Niesen, F.H. / Burgess, N. / Gileadi, O. / Gorrec, F. / Umeano, C. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human synapsin III (SYN3) in complex with AMPPNP
Authors: Turnbull, A.P. / Phillips, C. / Pike, A.C.W. / Elkins, J.M. / Gileadi, C. / Salah, E. / Niesen, F.H. / Burgess, N. / Gileadi, O. / Gorrec, F. / Umeano, C. / von Delft, F. / Weigelt, J. / ...Authors: Turnbull, A.P. / Phillips, C. / Pike, A.C.W. / Elkins, J.M. / Gileadi, C. / Salah, E. / Niesen, F.H. / Burgess, N. / Gileadi, O. / Gorrec, F. / Umeano, C. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Doyle, D.
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: Synapsin-3
B: Synapsin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,99120
Polymers76,8352
Non-polymers2,15618
Water8,035446
1
A: Synapsin-3
B: Synapsin-3
hetero molecules

A: Synapsin-3
B: Synapsin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,98240
Polymers153,6694
Non-polymers4,31236
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area21130 Å2
ΔGint-279 kcal/mol
Surface area43300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.796, 73.186, 78.398
Angle α, β, γ (deg.)90.00, 100.74, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: 4

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA90 - 14417 - 71
21GLNGLNBB90 - 14417 - 71
32PROPROAA155 - 39782 - 324
42PROPROBB155 - 39782 - 324
DetailsTetramer composed of chains A and B plus the 2 symmetry related chains generated by symmetry operator -X,Y,-Z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Synapsin-3 / / Synapsin III


Mass: 38417.305 Da / Num. of mol.: 2 / Fragment: Actin-binding and synaptic-vesicle binding region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Brain / Gene: SYN3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3/Rosetta / References: UniProt: O14994

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Non-polymers , 5 types, 464 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.26M (NH4)2SO4, 0.2M Li2SO4, Tris-HCl pH 8.5, 20 % Ethylene glycol added as cryoprotectant, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99991 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 21, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99991 Å / Relative weight: 1
ReflectionResolution: 1.9→64.28 Å / Num. all: 56940 / Num. obs: 56940 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.132
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.477 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swissmodel based on PDB entries: 1I7L, 1I7N, 1PK8

1i7l

1i7n

1pk8


Resolution: 1.9→47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.354 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21804 2801 4.9 %RANDOM
Rwork0.18131 ---
all0.18311 54131 --
obs0.18311 54131 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.433 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20.57 Å2
2--0.75 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 0 126 446 5223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224901
X-RAY DIFFRACTIONr_bond_other_d0.0020.023265
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9736642
X-RAY DIFFRACTIONr_angle_other_deg0.8823.0017945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.235602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63323.93201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09415817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8161520
X-RAY DIFFRACTIONr_chiral_restr0.080.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02979
X-RAY DIFFRACTIONr_nbd_refined0.1920.2842
X-RAY DIFFRACTIONr_nbd_other0.190.23432
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22268
X-RAY DIFFRACTIONr_nbtor_other0.0850.22403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2339
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.212
X-RAY DIFFRACTIONr_mcbond_it0.7411.53245
X-RAY DIFFRACTIONr_mcbond_other0.1711.51209
X-RAY DIFFRACTIONr_mcangle_it1.0124807
X-RAY DIFFRACTIONr_scbond_it1.70332140
X-RAY DIFFRACTIONr_scangle_it2.4194.51830
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3852 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.250.5
medium thermal0.472
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 210 -
Rwork0.264 3651 -
obs--90.83 %
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)
11.4631-0.0294-0.14420.74420.20630.6591-0.08750.1111-0.1427-0.01710.03770.01310.0904-0.06540.0498-0.0937-0.06230.0114-0.0826-0.0036-0.1232-9.8881-9.9166-19.6356
21.1816-0.10750.10510.7072-0.1880.7725-0.04190.04520.1248-0.02430.0213-0.0139-0.09840.05430.0206-0.106-0.04280.0054-0.1052-0.0137-0.114411.60411.2055-19.8296
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA90 - 14417 - 71
2X-RAY DIFFRACTION1AA155 - 39782 - 324
3X-RAY DIFFRACTION2BB90 - 14417 - 71
4X-RAY DIFFRACTION2BB155 - 39782 - 324

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