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- PDB-3q84: Crystal structure of human PACSIN 1 F-BAR domain -

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Basic information

Entry
Database: PDB / ID: 3q84
TitleCrystal structure of human PACSIN 1 F-BAR domain
ComponentsProtein kinase C and casein kinase substrate in neurons protein 1
KeywordsENDOCYTOSIS / Alpha helix / Cytoplasmic vesicle
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 / regulation of endocytosis / synaptic vesicle endocytosis / cytoskeletal protein binding ...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 / regulation of endocytosis / synaptic vesicle endocytosis / cytoskeletal protein binding / neuron projection morphogenesis / cytoskeleton organization / axon terminus / cytoplasmic vesicle membrane / actin filament organization / protein localization to plasma membrane / phospholipid binding / ruffle membrane / Clathrin-mediated endocytosis / endosome / synapse / perinuclear region of cytoplasm / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PACSIN1, F-BAR / PACSIN1/PACSIN2, SH3 domain / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR 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 / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR 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: 2.8 Å
AuthorsBai, X.
CitationJournal: To be Published
Title: Crystal structure of human PACSIN 1 F-BAR domain
Authors: Bai, X.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_leaving_atom_flag / _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_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
G: Protein kinase C and casein kinase substrate in neurons protein 1
H: Protein kinase C and casein kinase substrate in neurons protein 1
M: Protein kinase C and casein kinase substrate in neurons protein 1
N: Protein kinase C and casein kinase substrate in neurons protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,07410
Polymers212,9146
Non-polymers1604
Water3,837213
1
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)71,0113
Polymers70,9712
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-72 kcal/mol
Surface area32420 Å2
MethodPISA
2
G: Protein kinase C and casein kinase substrate in neurons protein 1
H: Protein kinase C and casein kinase substrate in neurons protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0113
Polymers70,9712
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-75 kcal/mol
Surface area32520 Å2
MethodPISA
3
M: Protein kinase C and casein kinase substrate in neurons protein 1
N: Protein kinase C and casein kinase substrate in neurons protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0514
Polymers70,9712
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-68 kcal/mol
Surface area30420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.346, 154.290, 215.446
Angle α, β, γ (deg.)90.00, 90.34, 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: 35485.594 Da / Num. of mol.: 6 / Fragment: hPACSIN 1 (UNP RESIDUES 14-308) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BY11
#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


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200mM NH4H2PO4, 100mM HEPES pH 7.5, 16% PEG 3350 (w/v), 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97924 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.8→29.06 Å / Num. all: 74726 / Num. obs: 63354 / % possible obs: 96.203 %
Reflection shellResolution: 2.83→2.91 Å / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.06 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.868 / SU B: 14.511 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29387 3358 5 %RANDOM
Rwork0.22145 ---
obs0.22507 63353 96.2 %-
all-74726 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20.13 Å2
2---0.47 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13874 0 4 213 14091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02214157
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.94218978
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18351668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87225.217759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.108152780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2111587
X-RAY DIFFRACTIONr_chiral_restr0.1210.21936
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210691
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7871.58383
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.639213367
X-RAY DIFFRACTIONr_scbond_it2.96735774
X-RAY DIFFRACTIONr_scangle_it4.9664.55611
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 207 -
Rwork0.305 4244 -
obs--87.43 %

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