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- PDB-3qni: Crystal structure of human PACSIN 1 F-BAR domain -

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Basic information

Entry
Database: PDB / ID: 3qni
TitleCrystal structure of human PACSIN 1 F-BAR domain
ComponentsProtein kinase C and casein kinase substrate in neurons protein 1
KeywordsENDOCYTOSIS / F-BAR 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMeng, G. / Bai, X. / Zheng, X.
CitationJournal: to be published
Title: Crystal structure of human PACSIN 1 F-BAR domain
Authors: Meng, G. / Bai, X. / Zheng, X.
History
DepositionFeb 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 1
B: Protein kinase C and casein kinase substrate in neurons protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6204
Polymers72,5402
Non-polymers802
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-75 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.899, 83.739, 86.511
Angle α, β, γ (deg.)90.00, 114.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 36269.969 Da / Num. of mol.: 2 / Fragment: F-BAR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PACSIN1 / Production host: Escherichia coli (E. coli) / 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.: 199 / 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: 3.36 Å3/Da / Density % sol: 63.42 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 22632 / Num. obs: 21232 / % possible obs: 93.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.902 / SU B: 31.107 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28376 1117 5 %RANDOM
Rwork0.20405 ---
obs0.20811 21232 93.78 %-
all-22632 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.478 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å2-7.35 Å2
2--0.22 Å20 Å2
3----9.24 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4461 0 2 199 4662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224554
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9426104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2875536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48525.143245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.4315901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1781528
X-RAY DIFFRACTIONr_chiral_restr0.1170.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023446
X-RAY DIFFRACTIONr_mcbond_it0.5551.52682
X-RAY DIFFRACTIONr_mcangle_it1.07724280
X-RAY DIFFRACTIONr_scbond_it1.88931872
X-RAY DIFFRACTIONr_scangle_it3.1684.51824
X-RAY DIFFRACTIONr_rigid_bond_restr1.18734554
X-RAY DIFFRACTIONr_sphericity_free5.283201
X-RAY DIFFRACTIONr_sphericity_bonded1.65634466
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 59 -
Rwork0.259 1136 -
obs--69.44 %
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)
10.81260.21971.26160.72471.45716.7776-0.0428-0.23930.01170.0927-0.02540.03850.1017-0.09650.06820.1525-0.03550.04820.11810.0050.215542.42116.186440.7424
20.88010.27161.57150.99222.38658.41910.00440.0960.0004-0.1377-0.07250.1005-0.0925-0.03010.0680.2061-0.05120.00660.05670.0080.242134.5591-6.65272.3803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 307
2X-RAY DIFFRACTION2B16 - 305

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