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- PDB-2x3w: structure of mouse syndapin I (crystal form 2) -

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Basic information

Entry
Database: PDB / ID: 2x3w
Titlestructure of mouse syndapin I (crystal form 2)
Components(PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1) x 2
KeywordsENDOCYTOSIS / 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 / synaptic vesicle endocytosis / cytoskeletal protein binding / neuron projection morphogenesis ...presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / Clathrin-mediated endocytosis / negative regulation of endocytosis / protein localization to membrane / synaptic vesicle endocytosis / cytoskeletal protein binding / neuron projection morphogenesis / axon terminus / cytoplasmic vesicle membrane / actin filament organization / phospholipid binding / ruffle membrane / myelin sheath / signal transduction / identical protein binding / cytoplasm / cytosol
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 / SH3 type barrels. / Src homology 3 domains / 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: 2.64 Å
AuthorsMa, Q. / Rao, Y. / 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: Refinement description / Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations / Other
Revision 1.3May 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

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)124,7804
Polymers124,7804
Non-polymers00
Water1,11762
1
A: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
B: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
D: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)85,4303
Polymers85,4303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-79.3 kcal/mol
Surface area44270 Å2
MethodPQS
2
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area8710 Å2
ΔGint-69 kcal/mol
Surface area29100 Å2
MethodPISA
3
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-76.8 kcal/mol
Surface area33110 Å2
MethodPISA
4
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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.280, 154.610, 191.740
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) / 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.: 1 / Fragment: SH3 DOMAIN, RESIDUES 382-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61644
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.2 Å3/Da / Density % sol: 44 % / 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 PH5.0, 3%(W/V) PEG4000., pH 5.3

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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: Oct 2, 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: 2.64→34.35 Å / Num. obs: 38766 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.17 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.81
Reflection shellResolution: 2.64→2.75 Å / Redundancy: 7.03 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.88 / % 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: 2.64→34.36 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 26.268 / SU ML: 0.257 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.624 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27373 1939 5 %THIN SHELLS
Rwork0.22066 ---
obs0.22335 36827 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: 30.357 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å20 Å2
2---6.14 Å20 Å2
3---4.09 Å2
Refinement stepCycle: LAST / Resolution: 2.64→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7449 0 0 62 7511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227594
X-RAY DIFFRACTIONr_bond_other_d00.025450
X-RAY DIFFRACTIONr_angle_refined_deg0.851.94610175
X-RAY DIFFRACTIONr_angle_other_deg0.6313232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2855893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92924.964415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.247151511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2261554
X-RAY DIFFRACTIONr_chiral_restr0.0490.21021
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028384
X-RAY DIFFRACTIONr_gen_planes_other00.021507
X-RAY DIFFRACTIONr_nbd_refined0.270.32078
X-RAY DIFFRACTIONr_nbd_other0.2320.35469
X-RAY DIFFRACTIONr_nbtor_refined0.1970.53714
X-RAY DIFFRACTIONr_nbtor_other0.0950.53946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.5278
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.55
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.349
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.3114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.97725920
X-RAY DIFFRACTIONr_mcbond_other0.3721816
X-RAY DIFFRACTIONr_mcangle_it2.46337132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.82843717
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5953043
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: 2.642→2.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 156 -
Rwork0.33 2623 -
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)
10.4717-2.122-0.044716.60372.49680.7537-0.02770.09060.0145-0.57120.5338-0.4872-0.09210.2192-0.506-0.19850.03350.0303-0.1172-0.0596-0.0031-5.5368-58.900824.7084
23.7771-4.33950.149210.68382.09720.9091-0.2991-0.08280.26160.93310.4532-0.4476-0.05160.2027-0.1541-0.01190.01760.0707-0.07750.0082-0.1585-11.4908-32.691937.4858
30.2661-0.1394-0.09612.1171.10250.5763-0.18990.17220.0037-0.0850.3643-0.1611-0.1710.421-0.1744-0.05490.037-0.0880.0141-0.1304-0.01051.0295-101.80426.3946
40.3811-1.377-0.883610.85834.74142.744-0.1315-0.0151-0.13580.76480.18430.05230.3960.0243-0.0529-0.20610.0379-0.1131-0.1586-0.04270.0414-9.8834-88.390522.5544
50.8510.3615-0.377911.45550.9890.2848-0.0011-0.1519-0.07761.64440.0236-0.42540.30220.1761-0.02240.22460.0728-0.01840.04630.0242-0.1351-20.6821-9.156146.154
60.7039-2.4956-1.271713.87883.88812.3745-0.2207-0.1907-0.18340.30480.7132-0.99430.09560.5148-0.4926-0.12080.0301-0.0345-0.081-0.0686-0.136-16.6147-3.640834.3195
73.4441-4.671-0.882317.21042.77962.39610.27490.2983-0.465-1.4933-0.1560.30690.07880.109-0.119-0.13210.08890.0479-0.0844-0.0339-0.1494-11.4516-48.556719.8981
80.7016-1.90110.352317.3288-0.96980.17690.13110.0706-0.2595-1.3907-0.0610.44250.0630.0802-0.070.01530.02660.0525-0.1017-0.0294-0.1748-21.3869-34.433321.6739
91.20111.15730.96863.72552.44862.9186-0.1123-0.03690.4328-0.66530.5519-0.4474-0.85080.9367-0.43960.1061-0.22580.2190.2844-0.27530.2259-8.381329.769146.993
100.2994-0.543-0.05285.11851.53760.54950.03-0.0339-0.1973-0.2623-0.06920.6073-0.04820.04460.0392-0.0612-0.02290.065-0.082-0.0389-0.0556-21.9648-31.219431.66
110.93771.40350.381612.61785.34032.3179-0.202-0.06390.3318-0.466-0.22381.1413-0.1449-0.06450.4258-0.04530.0476-0.051-0.1245-0.0361-0.154514.4628-61.95999.185
121.3372-0.0539-0.28197.57293.78472.6964-0.2258-0.24050.10760.6167-0.08440.940.2706-0.11280.3102-0.10720.0548-0.0034-0.0408-0.0439-0.19117.316-64.903815.1426
130.8693-2.51071.968624.2018-10.76417.85651.12931.05210.2284-0.3683-0.74951.85780.17330.8906-0.37980.34030.0930.10140.51230.0340.454511.231-5.582913.4451
140.6410.0551-0.00213.44831.33190.9516-0.1408-0.09830.17250.46110.2935-0.36840.16220.1443-0.1527-0.14120.00570.0158-0.0069-0.0176-0.19224.8996-63.26148.1943
1512.87062.0757-2.89485.67860.66620.89140.16790.23060.64-0.0996-0.2233-1.15870.17060.39870.05540.31940.0178-0.02150.58850.04810.4516-2.4207-6.044422.5588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 65
2X-RAY DIFFRACTION2A66 - 108
3X-RAY DIFFRACTION3A109 - 195
4X-RAY DIFFRACTION4A196 - 257
5X-RAY DIFFRACTION5A258 - 304
6X-RAY DIFFRACTION6B13 - 42
7X-RAY DIFFRACTION7B43 - 74
8X-RAY DIFFRACTION8B75 - 122
9X-RAY DIFFRACTION9B123 - 196
10X-RAY DIFFRACTION10B197 - 302
11X-RAY DIFFRACTION11C14 - 67
12X-RAY DIFFRACTION12C68 - 146
13X-RAY DIFFRACTION13C147 - 165
14X-RAY DIFFRACTION14C193 - 301
15X-RAY DIFFRACTION15D385 - 440

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