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- PDB-3hah: Crystal structure of human PACSIN1 F-BAR domain (C2 lattice) -

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Basic information

Entry
Database: PDB / ID: 3hah
TitleCrystal structure of human PACSIN1 F-BAR domain (C2 lattice)
Componentshuman PACSIN1 F-BAR
KeywordsENDOCYTOSIS / PACSIN / Syndapin / FAP52 / F-BAR / Coiled coil / Cytoplasm / Phosphoprotein / Polymorphism / SH3 domain
Function / homology
Function and homology information


presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / negative regulation of endocytosis / protein localization to membrane / positive regulation of dendrite development / synaptic vesicle endocytosis / regulation of endocytosis / axon terminus ...presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / negative regulation of endocytosis / protein localization to membrane / positive regulation of dendrite development / synaptic vesicle endocytosis / regulation of endocytosis / axon terminus / cytoskeleton organization / cytoskeletal protein binding / neuron projection morphogenesis / protein localization to plasma membrane / actin filament organization / cytoplasmic vesicle membrane / phospholipid binding / ruffle membrane / Clathrin-mediated endocytosis / endosome / synapse / perinuclear region of cytoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PACSIN1, F-BAR / 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 ...PACSIN1, F-BAR / 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
Protein kinase C and casein kinase substrate in neurons protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.77 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: human PACSIN1 F-BAR
B: human PACSIN1 F-BAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6694
Polymers76,5892
Non-polymers802
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-94 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.009, 85.457, 88.392
Angle α, β, γ (deg.)90.00, 117.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein human PACSIN1 F-BAR / Protein kinase C and casein kinase substrate in neurons protein 1


Mass: 38294.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1379, PACSIN1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY11
#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 / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 5

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2M potassium sodium tartrate tetrahydrate, 20% PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.77→48.07 Å / Num. all: 51664 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 86.9 Å2 / Net I/σ(I): 9.9
Reflection shellResolution: 2.77→3 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 7480 / % possible all: 27.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.77→48.07 Å / SU ML: 2.33 / σ(F): 1.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 2570 4.98 %
Rwork0.2147 --
all0.2169 51664 -
obs0.2169 51563 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.907 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 65.945 Å2
Baniso -1Baniso -2Baniso -3
1-29.794 Å20 Å2-13.882 Å2
2--3.013 Å20 Å2
3----32.807 Å2
Refinement stepCycle: LAST / Resolution: 2.77→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4449 0 2 60 4511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064537
X-RAY DIFFRACTIONf_angle_d0.9986081
X-RAY DIFFRACTIONf_dihedral_angle_d19.4311745
X-RAY DIFFRACTIONf_chiral_restr0.066613
X-RAY DIFFRACTIONf_plane_restr0.004790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.82340.3841920.36771765X-RAY DIFFRACTION64
2.8234-2.8810.43391460.3052774X-RAY DIFFRACTION100
2.881-2.94370.3151440.28042825X-RAY DIFFRACTION100
2.9437-3.01210.32351420.26722750X-RAY DIFFRACTION99
3.0121-3.08740.28181450.25622743X-RAY DIFFRACTION100
3.0874-3.17090.27211480.26712800X-RAY DIFFRACTION100
3.1709-3.26420.29561470.25732794X-RAY DIFFRACTION100
3.2642-3.36950.29621510.23882799X-RAY DIFFRACTION100
3.3695-3.48990.3261420.21882781X-RAY DIFFRACTION100
3.4899-3.62950.20211480.19642776X-RAY DIFFRACTION100
3.6295-3.79460.26491480.17942764X-RAY DIFFRACTION100
3.7946-3.99460.20111450.18582751X-RAY DIFFRACTION100
3.9946-4.24460.22611440.17362807X-RAY DIFFRACTION100
4.2446-4.57210.20431480.17512779X-RAY DIFFRACTION100
4.5721-5.03160.19451470.16682787X-RAY DIFFRACTION100
5.0316-5.75830.22081430.19672766X-RAY DIFFRACTION100
5.7583-7.24960.26191450.23412769X-RAY DIFFRACTION100
7.2496-43.97680.29741450.20892763X-RAY DIFFRACTION99

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