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- PDB-3q0k: Crystal structure of Human PACSIN 2 F-BAR -

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Basic information

Entry
Database: PDB / ID: 3q0k
TitleCrystal structure of Human PACSIN 2 F-BAR
ComponentsProtein kinase C and casein kinase substrate in neurons protein 2
KeywordsENDOCYTOSIS / alpha helix / membrane remodeling / Cytoplasmic vesicle
Function / homology
Function and homology information


caveola assembly / cell projection morphogenesis / plasma membrane tubulation / protein localization to endosome / phosphatidic acid binding / negative regulation of endocytosis / caveolin-mediated endocytosis / regulation of endocytosis / centriolar satellite / cytoskeleton organization ...caveola assembly / cell projection morphogenesis / 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 / caveola / phospholipid binding / modulation of chemical synaptic transmission / ruffle membrane / recycling endosome membrane / cell-cell junction / Clathrin-mediated endocytosis / actin cytoskeleton organization / early endosome / endosome / nuclear speck / cadherin binding / focal adhesion / intracellular membrane-bounded organelle / 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 / 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: 2.6 Å
AuthorsBai, X. / Meng, G. / Zheng, X.
CitationJournal: To be Published
Title: Crystal structure of human PACSIN 2 F-BAR domain
Authors: Bai, X. / Meng, G. / Zheng, X.
History
DepositionDec 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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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
C: Protein kinase C and casein kinase substrate in neurons protein 2
D: Protein kinase C and casein kinase substrate in neurons protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,3258
Polymers137,1644
Non-polymers1604
Water3,639202
1
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)68,6624
Polymers68,5822
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-63 kcal/mol
Surface area32790 Å2
MethodPISA
2
C: Protein kinase C and casein kinase substrate in neurons protein 2
D: Protein kinase C and casein kinase substrate in neurons protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6624
Polymers68,5822
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-66 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.562, 353.588, 86.045
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34291.090 Da / Num. of mol.: 4 / Fragment: F-BAR domain, UNP residues 16-304
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.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MgCl2, 100mM NaCacodylate pH 6.5, 18% PEG 3350 (w/v), VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 44004 / % possible obs: 5.0861 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.7 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HAJ

3haj


Resolution: 2.6→29.63 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.817 / SU B: 24.545 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2918 2358 5.1 %RANDOM
Rwork0.20143 ---
all0.2202 ---
obs0.206 44004 80.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.611 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.06 Å2
2--0.06 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9523 0 4 202 9729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229801
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.93813125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42351152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7524.728533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.191151941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.341568
X-RAY DIFFRACTIONr_chiral_restr0.1180.21308
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027453
X-RAY DIFFRACTIONr_mcbond_it0.7591.55760
X-RAY DIFFRACTIONr_mcangle_it1.43429179
X-RAY DIFFRACTIONr_scbond_it2.4434041
X-RAY DIFFRACTIONr_scangle_it3.9884.53946
X-RAY DIFFRACTIONr_rigid_bond_restr1.2639801
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 80 -
Rwork0.22 1407 -
obs--35.36 %

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