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- PDB-2x3x: structure of mouse syndapin I (crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 2x3x
Titlestructure of mouse syndapin I (crystal form 1)
Components(PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1) x 2
KeywordsENDOCYTOSIS / PHOSPHOPROTEIN / BAR / N-WASP / DYNAMIN / PACSIN I / TRANSFERASE
Function / homology
Function and homology information


presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / Clathrin-mediated endocytosis / negative regulation of endocytosis / protein localization to membrane / neuron projection morphogenesis / synaptic vesicle endocytosis / cytoskeletal protein binding ...presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / Clathrin-mediated endocytosis / negative regulation of endocytosis / protein localization to membrane / neuron projection morphogenesis / synaptic vesicle endocytosis / cytoskeletal protein binding / axon terminus / cytoplasmic vesicle membrane / actin filament organization / phospholipid binding / ruffle membrane / myelin sheath / signal transduction / identical protein binding / cytosol / cytoplasm
Similarity search - Function
PACSIN1, F-BAR / PACSIN1/PACSIN2, SH3 domain / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain ...PACSIN1, F-BAR / PACSIN1/PACSIN2, SH3 domain / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein kinase C and casein kinase substrate in neurons protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsMa, Q. / Rao, Y. / Vahedi-Faridi, A. / Saenger, W. / Haucke, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Molecular Basis for SH3 Domain Regulation of F-Bar-Mediated Membrane Deformation.
Authors: Rao, Y. / Ma, Q. / Vahedi-Faridi, A. / Sundborger, A. / Pechstein, A. / Puchkov, D. / Luo, L. / Shupliakov, O. / Saenger, W. / Haucke, V.
History
DepositionJan 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
B: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
C: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
D: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
E: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)131,5115
Polymers131,5115
Non-polymers00
Water00
1
C: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1

C: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)78,6992
Polymers78,6992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area9310 Å2
ΔGint-72 kcal/mol
Surface area32700 Å2
MethodPISA
2
A: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
B: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)78,6992
Polymers78,6992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-77.3 kcal/mol
Surface area31440 Å2
MethodPISA
3
D: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)6,7311
Polymers6,7311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)6,7311
Polymers6,7311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.077, 154.545, 255.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1 / SYNDAPIN I


Mass: 39349.430 Da / Num. of mol.: 3 / Fragment: F-BAR DOMAIN, RESIDUES 1-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61644
#2: Protein PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1 / SYNDAPIN I


Mass: 6731.324 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 382-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61644

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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: 2.76 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 5.3
Details: 2.5UL SYNDAPIN (5MG/ML IN 50MM HEPES, 50MM NACL) MIXED WITH 0.5UL 0.3M GLYCYL-GLYCYL-GLYCINE AND 2UL WELL SOLUTION 0.1M NAAC/HAC PH5.3, 3%(W/V) PEG4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2009
Details: DOUBLE CRYSTAL MONOCHROMATOR WITH 2 SETS OF MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.35→73.17 Å / Num. obs: 23772 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 6.11 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.97
Reflection shellResolution: 3.35→3.45 Å / Redundancy: 6.16 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.62 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→73.13 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.884 / SU B: 46.502 / SU ML: 0.312 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.562 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27701 1192 5 %THIN SHELLS
Rwork0.22062 ---
obs0.2234 22578 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.581 Å2
Baniso -1Baniso -2Baniso -3
1-12.02 Å20 Å20 Å2
2---11.66 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 3.35→73.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8006 0 0 0 8006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228162
X-RAY DIFFRACTIONr_bond_other_d0.0010.025831
X-RAY DIFFRACTIONr_angle_refined_deg0.9721.94810945
X-RAY DIFFRACTIONr_angle_other_deg0.774314158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.555962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32424.989447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.482151604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3581558
X-RAY DIFFRACTIONr_chiral_restr0.0520.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021620
X-RAY DIFFRACTIONr_nbd_refined0.2130.22208
X-RAY DIFFRACTIONr_nbd_other0.1650.26093
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23824
X-RAY DIFFRACTIONr_nbtor_other0.0850.24458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2195
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.257
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1670.2151
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.08425045
X-RAY DIFFRACTIONr_mcbond_other0.15521958
X-RAY DIFFRACTIONr_mcangle_it1.77837679
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.86843722
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.87553266
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.35→3.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 121 -
Rwork0.333 1610 -
obs--100 %
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)
10.16150.2451-0.1999.1634-2.99891.6406-0.0331-0.04780.02910.32640.21630.0123-0.2064-0.335-0.1832-0.4297-0.06840.0304-0.32210.0382-0.4305-27.881953.0194-49.2242
20.57810.5659-0.32516.2443-1.75650.7999-0.103-0.1709-0.1817-0.27390.2510.28760.1025-0.1614-0.148-0.1831-0.1958-0.0801-0.29070.0694-0.3928-35.43467.3712-41.4692
30.4294-0.12810.10224.5568-2.281.5291-0.25760.07110.0243-0.61620.3075-0.77980.1158-0.1061-0.0498-0.0176-0.09050.1897-0.0510.1501-0.0321-18.1643-57.1197-15.2569
43.31821.11081.47467.5219-4.60379.7439-0.2602-1.12980.33830.89050.1128-0.6432-0.7997-0.45720.14740.57860.1240.08090.0413-0.2376-0.0822-22.7706103.6314-49.9957
52.9334-2.40271.44647.0814.1616.3022-0.3775-0.39370.43080.95870.4515-0.1114-0.41860.0927-0.07410.6491-0.15930.11190.47320.05750.291-41.301723.6153-19.7659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 304
2X-RAY DIFFRACTION2B13 - 304
3X-RAY DIFFRACTION3C14 - 304
4X-RAY DIFFRACTION4D385 - 440
5X-RAY DIFFRACTION5E385 - 440

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