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- PDB-1zww: Crystal structure of endophilin-A1 BAR domain -

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Basic information

Entry
Database: PDB / ID: 1zww
TitleCrystal structure of endophilin-A1 BAR domain
ComponentsSH3-containing GRB2-like protein 2
KeywordsTRANSFERASE / coiled coil
Function / homology
Function and homology information


postsynaptic actin cytoskeleton organization / Negative regulation of MET activity / EGFR downregulation / Retrograde neurotrophin signalling / Lysosome Vesicle Biogenesis / negative regulation of blood-brain barrier permeability / dendrite extension / Recycling pathway of L1 / regulation of receptor internalization / photoreceptor ribbon synapse ...postsynaptic actin cytoskeleton organization / Negative regulation of MET activity / EGFR downregulation / Retrograde neurotrophin signalling / Lysosome Vesicle Biogenesis / negative regulation of blood-brain barrier permeability / dendrite extension / Recycling pathway of L1 / regulation of receptor internalization / photoreceptor ribbon synapse / Golgi Associated Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / MHC class II antigen presentation / negative regulation of epidermal growth factor receptor signaling pathway / synaptic vesicle endocytosis / negative regulation of MAPK cascade / presynaptic cytosol / cellular response to brain-derived neurotrophic factor stimulus / cell projection / neuron projection development / early endosome / postsynapse / negative regulation of gene expression / lipid binding / perinuclear region of cytoplasm / glutamatergic synapse / identical protein binding / membrane
Similarity search - Function
Endophilin-A, SH3 domain / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / : / BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain ...Endophilin-A, SH3 domain / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / : / BAR domain / AH/BAR domain superfamily / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWeissenhorn, W.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of the Endophilin-A1 BAR Domain.
Authors: Weissenhorn, W.
History
DepositionJun 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.ptnr3_symmetry / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: SH3-containing GRB2-like protein 2
B: SH3-containing GRB2-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,91613
Polymers58,6792
Non-polymers1,23711
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-116 kcal/mol
Surface area19700 Å2
MethodPISA
2
A: SH3-containing GRB2-like protein 2
B: SH3-containing GRB2-like protein 2
hetero molecules

A: SH3-containing GRB2-like protein 2
B: SH3-containing GRB2-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,83126
Polymers117,3584
Non-polymers2,47322
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area15320 Å2
ΔGint-249 kcal/mol
Surface area37270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.705, 121.651, 244.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SH3-containing GRB2-like protein 2 / SH3 domain protein 2A / Endophilin 1 / SH3p4


Mass: 29339.547 Da / Num. of mol.: 2 / Fragment: endophilin BAR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sh3gl2, Sh3d2a / Plasmid: petM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+
References: UniProt: Q62420, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: sodium acetate, cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 9.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97879
DetectorDate: Mar 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 2.3→48.7 Å / Num. obs: 27463

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.601data extraction
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.459 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1379 5 %RANDOM
Rwork0.249 ---
obs0.251 26035 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.03 Å2
Baniso -1Baniso -2Baniso -3
1-4.09 Å20 Å20 Å2
2---0.12 Å20 Å2
3----3.98 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 11 69 3060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213014
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9774066
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2255390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62225.319141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63915523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3551519
X-RAY DIFFRACTIONr_chiral_restr0.0980.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022261
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21396
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.22105
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3430.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3060.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 97 -
Rwork0.275 1756 -
obs--93.21 %

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