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- PDB-4bne: Pacsin2 Interacts with Membranes and Actin-Filaments -

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Basic information

Entry
Database: PDB / ID: 4bne
TitlePacsin2 Interacts with Membranes and Actin-Filaments
ComponentsPROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 2
KeywordsENDOCYTOSIS / MEMBRANE SCULPTING / F- ACTIN BINDING
Function / homology
Function and homology information


caveola assembly / plasma membrane tubulation / phosphatidic acid binding / negative regulation of endocytosis / regulation of endocytosis / cytoskeleton organization / cytoskeletal protein binding / caveola / cytoplasmic vesicle membrane / phospholipid binding ...caveola assembly / plasma membrane tubulation / phosphatidic acid binding / negative regulation of endocytosis / regulation of endocytosis / cytoskeleton organization / cytoskeletal protein binding / caveola / cytoplasmic vesicle membrane / phospholipid binding / ruffle membrane / endocytosis / recycling endosome membrane / actin cytoskeleton organization / early endosome / cytoskeleton / endosome / focal adhesion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein kinase C and casein kinase substrate in neurons protein 2 / PACSIN2, F-BAR domain / PACSIN1/PACSIN2, SH3 domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily ...Protein kinase C and casein kinase substrate in neurons protein 2 / PACSIN2, F-BAR domain / PACSIN1/PACSIN2, SH3 domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Protein kinase C and casein kinase substrate in neurons protein 2
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.57 Å
AuthorsKostan, J. / Salzer, U. / Orlova, A. / Toeroe, I. / Hodnik, V. / Schreiner, C. / Merilainen, J. / Nikki, M. / Virtanen, I. / Lehto, V.-P. ...Kostan, J. / Salzer, U. / Orlova, A. / Toeroe, I. / Hodnik, V. / Schreiner, C. / Merilainen, J. / Nikki, M. / Virtanen, I. / Lehto, V.-P. / Anderluh, G. / Egelman, E.H. / Djinovic-Carugo, K.
CitationJournal: Embo Rep. / Year: 2014
Title: Direct Interaction of Actin Filaments with F-Bar Protein Pacsin2.
Authors: Kostan, J. / Salzer, U. / Orlova, A. / Toro, I. / Hodnik, V. / Senju, Y. / Zou, J. / Schreiner, C. / Steiner, J. / Merilainen, J. / Nikki, M. / Virtanen, I. / Carugo, O. / Rappsilber, J. / ...Authors: Kostan, J. / Salzer, U. / Orlova, A. / Toro, I. / Hodnik, V. / Senju, Y. / Zou, J. / Schreiner, C. / Steiner, J. / Merilainen, J. / Nikki, M. / Virtanen, I. / Carugo, O. / Rappsilber, J. / Lappalainen, P. / Lehto, V. / Anderluh, G. / Egelman, E.H. / Djinovic-Carugo, K.
History
DepositionMay 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 2
B: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,78411
Polymers105,8112
Non-polymers9739
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-139.3 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.060, 105.500, 125.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9728, -0.2317, 0.004372), (-0.2317, 0.9722, -0.03496), (0.003847, -0.03502, -0.9994)
Vector: 273.5, 32.33, 11.78)

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Components

#1: Protein PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 2 / FOCAL ADHESION PROTEIN OF 52 KDA / FAP52 / PACSIN2


Mass: 52905.723 Da / Num. of mol.: 2 / Fragment: F-BAR DOMAIN
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL PROTEOLYTIC FRAGMENT COMPRISING THE WHOLE F-BAR DOMAIN
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O13154
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1,4,7,10-TETRAOXA-DECAN (PGE): PEG FRAGMENT SULFATE ION (SO4): C 2, C 3, C 4, C 5, C 6, C 7 ...1,4,7,10-TETRAOXA-DECAN (PGE): PEG FRAGMENT SULFATE ION (SO4): C 2, C 3, C 4, C 5, C 6, C 7 RESIDUES REFINED WITH OCCUPANCY LT 1.0

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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: 4.81 Å3/Da / Density % sol: 74.5 % / Description: NONE
Crystal growpH: 8 / Details: PEG2000MME, AMMONIUM SULFATE, HEPES PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.57→53.45 Å / Num. obs: 41812 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 49.92 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.12
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.25 / % possible all: 77.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.57→53.447 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 24.58 / Stereochemistry target values: ML / Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2222 2111 5.1 %
Rwork0.1838 --
obs0.1858 41803 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.2057 Å2 / ksol: 0.0887 e/Å3
Displacement parametersBiso mean: 64.6 Å2
Refinement stepCycle: LAST / Resolution: 2.57→53.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 55 185 5056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024958
X-RAY DIFFRACTIONf_angle_d0.5156635
X-RAY DIFFRACTIONf_dihedral_angle_d13.4721935
X-RAY DIFFRACTIONf_chiral_restr0.035663
X-RAY DIFFRACTIONf_plane_restr0.002858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5701-2.62990.31611140.28952060X-RAY DIFFRACTION76
2.6299-2.69560.30681120.27982251X-RAY DIFFRACTION83
2.6956-2.76850.30111340.26652436X-RAY DIFFRACTION90
2.7685-2.850.30931260.24872647X-RAY DIFFRACTION97
2.85-2.9420.29591360.22292733X-RAY DIFFRACTION100
2.942-3.04710.23661520.2212700X-RAY DIFFRACTION99
3.0471-3.16910.27831430.22422723X-RAY DIFFRACTION100
3.1691-3.31330.24361380.2262731X-RAY DIFFRACTION100
3.3133-3.48790.21341490.19452731X-RAY DIFFRACTION100
3.4879-3.70640.23921400.16712731X-RAY DIFFRACTION100
3.7064-3.99250.20691390.15212743X-RAY DIFFRACTION100
3.9925-4.39410.18291520.15132776X-RAY DIFFRACTION100
4.3941-5.02960.15971590.14132755X-RAY DIFFRACTION99
5.0296-6.33510.22251590.18092785X-RAY DIFFRACTION99
6.3351-53.45870.21211580.16852890X-RAY DIFFRACTION98
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)
1-0.01860.02270.0318-0.0251-0.0031-0.01390.07960.0082-0.1377-0.0427-0.27630.0735-0.06560.0287-00.14940.0144-0.01040.03810.13930.1841137.5774115.656114.5699
2-0.0002-0.0024-0.00020.00770.00960.0038-0.0519-0.01450.0042-0.0622-0.00330.01080.04330.0598-00.26470.0044-0.01270.2840.04740.2821136.1071119.55662.0527
30.02860.01420.00210.0034-0.00090.0025-0.04790.0424-0.0169-0.01780.01470.0366-0.01250.0062-00.3685-0.1217-0.12620.52710.30210.0638164.9318116.538668.761
4-0.00040.00220.00360.0066-0.0002-0.0014-0.0137-0.03750.00060.0054-0.02360.06150.00350.0402-00.2136-0.1114-0.04480.14730.05310.2734150.0313128.819227.7407
50.00150.0057-0.00050.0031-0.0027-0.001-0.09330.0713-0.03130.0329-0.1039-0.1052-0.0048-0.019400.23290.0335-0.04820.2270.0650.3403109.0455124.5614-24.0197
60.0258-0.0429-0.007-0.02230.0263-0.00110.0608-0.029-0.0217-0.0052-0.1175-0.003-0.0142-0.0569-00.2759-0.066-0.02010.2601-0.02450.2588115.0187115.43880.8144
70.02960.00880.02190.0257-0.01010.0029-0.03590.08560.11370.041-0.1914-0.1412-0.0267-0.0733-00.20060.16980.05060.3003-0.22540.043390.1455109.9525-45.3372
80.0105-0.0068-0.0110.0074-0.00120.0019-0.0751-0.0997-0.0166-0.079-0.08350.1364-0.00330.048600.268-0.0373-0.01330.312-0.03490.2933138.133129.322130.9753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 15 THROUGH 72 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 73 THROUGH 128 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 129 THROUGH 218 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 219 THROUGH 255 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 256 THROUGH 304 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 15 THROUGH 119 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 120 THROUGH 255 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 256 THROUGH 303 )

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