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- PDB-3haj: Crystal structure of human PACSIN2 F-BAR domain (p212121 lattice) -

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Basic information

Entry
Database: PDB / ID: 3haj
TitleCrystal structure of human PACSIN2 F-BAR domain (p212121 lattice)
Componentshuman PACSIN2 F-BAR
KeywordsENDOCYTOSIS / PACSIN / Syndapin / FAP52 / F-BAR / Alternative splicing / Coiled coil / Cytoplasmic vesicle / Phosphoprotein / Polymorphism / SH3 domain
Function / homology
Function and homology information


cell projection morphogenesis / caveola assembly / plasma membrane tubulation / protein localization to endosome / phosphatidic acid binding / negative regulation of endocytosis / caveolin-mediated endocytosis / regulation of endocytosis / centriolar satellite / cytoskeleton organization ...cell projection morphogenesis / caveola assembly / plasma membrane tubulation / protein localization to endosome / phosphatidic acid binding / negative regulation of endocytosis / caveolin-mediated endocytosis / regulation of endocytosis / centriolar satellite / cytoskeleton organization / cytoskeletal protein binding / modulation of chemical synaptic transmission / caveola / phospholipid binding / ruffle membrane / recycling endosome membrane / cell-cell junction / Clathrin-mediated endocytosis / actin cytoskeleton organization / early endosome / endosome / nuclear speck / cadherin binding / intracellular membrane-bounded organelle / focal adhesion / glutamatergic synapse / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsWang, Q. / Navarro, M.V.A.S. / Peng, G. / Rajashankar, K.R. / Sondermann, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Molecular mechanism of membrane constriction and tubulation mediated by the F-BAR protein Pacsin/Syndapin.
Authors: Wang, Q. / Navarro, M.V. / Peng, G. / Molinelli, E. / Lin Goh, S. / Judson, B.L. / Rajashankar, K.R. / Sondermann, H.
History
DepositionMay 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: human PACSIN2 F-BAR
B: human PACSIN2 F-BAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7154
Polymers111,6352
Non-polymers802
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-71 kcal/mol
Surface area32530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.295, 88.395, 357.722
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 human PACSIN2 F-BAR / Protein kinase C and casein kinase substrate in neurons protein 2


Mass: 55817.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PACSIN2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UNF0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG-MME 5000, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.78→44.72 Å / Num. all: 25179 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 78.8 Å2 / Net I/σ(I): 14.2
Reflection shellResolution: 2.78→2.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 3092 / % possible all: 30.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HAI

3hai


Resolution: 2.78→44.715 Å / SU ML: 2.2 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 1259 5 %RANDOM
Rwork0.2241 ---
all0.2265 25179 --
obs0.2265 25178 95.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.3 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 78.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.501 Å2-0 Å2-0 Å2
2---0.842 Å20 Å2
3----12.487 Å2
Refinement stepCycle: LAST / Resolution: 2.78→44.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4715 0 2 36 4753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034812
X-RAY DIFFRACTIONf_angle_d0.6726440
X-RAY DIFFRACTIONf_dihedral_angle_d20.3391863
X-RAY DIFFRACTIONf_chiral_restr0.051646
X-RAY DIFFRACTIONf_plane_restr0.003840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.89160.4081130.34352147X-RAY DIFFRACTION79
2.8916-3.02320.30211390.2462640X-RAY DIFFRACTION98
3.0232-3.18250.28721420.23332707X-RAY DIFFRACTION98
3.1825-3.38190.28111410.22172682X-RAY DIFFRACTION98
3.3819-3.64290.25951410.19952684X-RAY DIFFRACTION98
3.6429-4.00930.25881440.19562729X-RAY DIFFRACTION97
4.0093-4.58890.20491430.18452711X-RAY DIFFRACTION98
4.5889-5.77960.22371440.19322738X-RAY DIFFRACTION97
5.7796-44.7210.29521520.24512881X-RAY DIFFRACTION95

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