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- PDB-3lll: Crystal structure of mouse pacsin2 F-BAR domain -

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Basic information

Entry
Database: PDB / ID: 3lll
TitleCrystal structure of mouse pacsin2 F-BAR domain
ComponentsProtein kinase C and casein kinase substrate in neurons protein 2
KeywordsENDOCYTOSIS / coiled-coil / membrane fusion / vesicular traffic / Cytoplasmic vesicle / Phosphoprotein / SH3 domain
Function / homology
Function and homology information


caveola assembly / cell projection morphogenesis / plasma membrane tubulation / protein localization to endosome / Clathrin-mediated endocytosis / phosphatidic acid binding / negative regulation of endocytosis / caveolin-mediated endocytosis / extrinsic component of membrane / regulation of endocytosis ...caveola assembly / cell projection morphogenesis / plasma membrane tubulation / protein localization to endosome / Clathrin-mediated endocytosis / phosphatidic acid binding / negative regulation of endocytosis / caveolin-mediated endocytosis / extrinsic component of membrane / regulation of endocytosis / cytoskeleton organization / cytoskeletal protein binding / caveola / cytoplasmic vesicle membrane / phospholipid binding / ruffle membrane / recycling endosome membrane / cell-cell junction / actin cytoskeleton organization / early endosome / cytoskeleton / endosome / nuclear speck / intracellular membrane-bounded organelle / lipid binding / signal transduction / identical protein binding / plasma membrane / cytosol / cytoplasm
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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain / 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
Protein kinase C and casein kinase substrate in neurons protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsRudolph, M.G.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A hinge in the distal end of the PACSIN 2 F-BAR domain may contribute to membrane-curvature sensing.
Authors: Plomann, M. / Wittmann, J.G. / Rudolph, M.G.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_asym_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_asym_id / _struct_conn.ptnr2_label_asym_id / _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)68,76512
Polymers68,0382
Non-polymers72710
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-182 kcal/mol
Surface area33700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.390, 106.400, 125.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein kinase C and casein kinase substrate in neurons protein 2


Mass: 34018.852 Da / Num. of mol.: 2 / Fragment: F-BAR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pacsin2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WVE8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 5.1 Å3/Da / Density % sol: 75.89 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 mixture of 20mg/mL mPACSIN2 and reservoir containing 0.1M HEPES/NaOH pH7.5, 1.62-1.66M (NH4)2SO4, 0.03M KBr, 4-4.5% PEG-MME 550, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 7, 2007 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.3→52.2 Å / Num. obs: 20356 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 47 Å2 / Rsym value: 0.033 / Net I/σ(I): 3.9
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 2973 / Rsym value: 0.438 / % possible all: 96.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3haj (human PACSIN 2)

3haj


Resolution: 3.3→52.195 Å / SU ML: 2.29 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.297 892 4.97 %random
Rwork0.2557 ---
obs0.2577 17953 83.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.666 Å2 / ksol: 0.304 e/Å3
Refinement stepCycle: LAST / Resolution: 3.3→52.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 34 0 4806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014892
X-RAY DIFFRACTIONf_angle_d0.4026554
X-RAY DIFFRACTIONf_dihedral_angle_d11.1141890
X-RAY DIFFRACTIONf_chiral_restr0.03662
X-RAY DIFFRACTIONf_plane_restr0.002846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.50690.39351400.3452574X-RAY DIFFRACTION77
3.5069-3.77760.34851320.30032780X-RAY DIFFRACTION82
3.7776-4.15760.28571370.26492831X-RAY DIFFRACTION84
4.1576-4.75880.26891540.22392941X-RAY DIFFRACTION86
4.7588-5.99420.28171650.22072915X-RAY DIFFRACTION85
5.9942-52.20150.24961640.21783020X-RAY DIFFRACTION85
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined2.91681.8201-2.52512.9228-1.69193.02030.14040.2892-0.0279-0.22880.085-0.14891.46410.57980.1410.58970.1914-0.07890.74420.16120.55973.4004-12.5042-43.7872
24.15670.4503-0.97752.9331-0.15263.62320.3701-0.57210.53480.4401-0.19640.1656-0.95030.48420.0090.5215-0.0793-0.17810.5421-0.07760.4538
32.51821.2247-3.58771.3967-1.5184.65880.341-0.68560.24870.2022-0.23190.1421-0.52340.90130.29580.5271-0.0244-0.14651.26650.09680.6005
49.20258.59220.60686.69925.5325-4.8014-2.61411.09382.1596-1.97990.7893.28441.33750.9914-0.14841.59040.11050.02741.22250.26361.2729
52.023-6.64682.53749.9846-2.21456.5776-0.6495-0.5455-0.0692-3.92320.5147-1.40271.09923.085-1.5492.48980.29230.08441.8535-0.00350.2024
61.7301-0.0318-1.34461.0456-0.1363-0.07823.50391.77883.1121-1.95890.0031.9135-1.1277-1.0724-0.00722.65630.4720.96211.569-0.01211.6044
71.6086-1.7056-2.05629.74732.48661.1462-2.9764-1.1757-1.19992.73910.51230.9261-2.3062.19140.09080.8507-0.0951-0.16252.86060.07410.8565
85.27441.5179-3.58232.3257-2.15161.524-0.864-0.191-1.0247-0.3724-0.4036-0.78460.97440.64780.36590.57090.1331-0.06180.6430.10780.7565
92.8264-0.2935-2.46742.4067-1.01894.45730.1548-0.067-1.1261-1.68170.126-1.87761.50722.54590.38390.7402-0.12770.00660.71160.04671.1516
109.2581-2.2318-8.68762.42982.05437.0126-0.3084-1.49980.80420.83440.6943-0.00431.32022.37360.44130.57670.0563-0.13170.92670.04050.3718
113.4269-0.533-3.2107-0.00250.56441.30140.0943-0.2053-0.13280.104-0.18740.0965-0.31320.05240.09380.4012-0.04610.00570.6629-0.03190.3621
129.7526-0.3977-2.40042.4514-3.70614.52680.10692.2737-1.2513-0.2367-0.5416-0.1220.605-0.3957-0.16590.2392-0.0473-0.1690.726-0.2390.3517
130.7725-0.7893-0.50312.67980.6207-2.02090.1787-0.0220.027-0.1748-0.43060.2696-0.6919-0.07240.2750.647-0.0645-0.08121.0703-0.19540.7433
146.70742.1832-7.68629.0812-1.71717.7926-0.1324-2.98172.015-0.0437-1.2778-0.3851-1.02821.086-5.57491.26650.30580.77261.0538-0.28051.3447
157.1831-3.7844-4.87916.45978.92947.7838-0.31230.8093-0.1918-0.26410.5934-1.08440.6805-0.46672.14752.30820.2058-0.06520.1079-0.21351.4253
168.62595.8240.58386.8162-0.85020.96521.9632-0.9738-1.1331.53592.2804-3.1496-0.91971.29070.2840.94041.0314-0.05232.0893-0.92872.3617
171.12621.5574-0.72581.2849-0.00770.12571.0107-1.27870.27220.0265-0.6137-2.39392.2652-1.21360.24111.35430.57030.02921.6676-0.00730.7523
184.9651-1.4751-6.3271.05060.79987.87360.22690.401-0.38920.3554-0.30070.1198-0.4281-1.39280.4770.7235-0.098-0.10591.0436-0.19210.7231
192.16851.5487-0.83336.1271-3.99165.94190.2225-0.34290.24440.83370.1091-0.1171-0.9144-0.8732-1.24180.28390.0873-0.1172-0.18090.03240.6892
201.7372-0.5251-0.31760.21-0.59480.70180.42780.73510.7744-0.7264-0.2651-0.5504-0.767-0.7094-0.08271.03560.13450.13261.40290.040.7759
Refinement TLS groupSelection details: chain B and resid 289:303)

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