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- PDB-3c0c: X-ray Crystal Structure of the Rat Endophilin A2 SH3 Domain -

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Basic information

Entry
Database: PDB / ID: 3c0c
TitleX-ray Crystal Structure of the Rat Endophilin A2 SH3 Domain
ComponentsEndophilin-A2
KeywordsENDOCYTOSIS / SH3 / voltage-gated calcium channel / Endosome / Lipid-binding / Membrane / Phosphoprotein / Proto-oncogene / SH3 domain
Function / homology
Function and homology information


Negative regulation of MET activity / EGFR downregulation / beta-1 adrenergic receptor binding / synaptic vesicle uncoating / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / anchoring junction / podosome / regulation of synaptic vesicle endocytosis ...Negative regulation of MET activity / EGFR downregulation / beta-1 adrenergic receptor binding / synaptic vesicle uncoating / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / anchoring junction / podosome / regulation of synaptic vesicle endocytosis / modulation of excitatory postsynaptic potential / postsynaptic density, intracellular component / phosphatase binding / hippocampal mossy fiber to CA3 synapse / cell projection / Schaffer collateral - CA1 synapse / SH3 domain binding / GTPase binding / presynapse / early endosome membrane / transmembrane transporter binding / lipid binding / glutamatergic synapse / synapse / identical protein binding / cytoplasm
Similarity search - Function
Endophilin-A, SH3 domain / BAR domain / BAR domain profile. / BAR / : / BAR domain / AH/BAR domain superfamily / SH3 Domains / SH3 domain / SH3 type barrels. ...Endophilin-A, SH3 domain / BAR domain / BAR domain profile. / BAR / : / BAR domain / AH/BAR domain superfamily / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsLoll, P.J. / Swain, E.
CitationJournal: To be Published
Title: Crystal structure of the SH3 domain of rat endophilin A2
Authors: Loll, P.J. / Swain, E. / Chen, Y. / Turner, B.T. / Zhang, J.
History
DepositionJan 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endophilin-A2


Theoretical massNumber of molelcules
Total (without water)8,2991
Polymers8,2991
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.970, 64.970, 41.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Endophilin-A2 / Endophilin-2 / SH3 domain-containing GRB2-like protein 1 / SH3 domain protein 2B / Extra eleven- ...Endophilin-2 / SH3 domain-containing GRB2-like protein 1 / SH3 domain protein 2B / Extra eleven-nineteen leukemia fusion gene protein / EEN / EEN fusion partner of MLL


Mass: 8299.041 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sh3gl1, Sh3p8 / Plasmid: GST-parallel / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O35964
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 277 K / Method: hanging drop vapor diffusion / pH: 6.5
Details: 1.9 M magnesium sulfate, 0.1 M MES, pH 6.5, hanging drop vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9000, 0.9795, 0.9798
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97951
30.97981
ReflectionResolution: 1.41→34.89 Å / Num. obs: 13188 / % possible obs: 75.2 % / Redundancy: 9.04 % / Rmerge(I) obs: 0.081 / Χ2: 0.92 / Net I/σ(I): 11 / Scaling rejects: 1668
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.41-1.461.230.620.72802261.7513.3
1.46-1.521.810.6860.512396771.639.4
1.52-1.592.880.7170.6312910561.3961
1.59-1.684.140.6661569713561.5478.3
1.68-1.785.730.6021.5912815501.4790.1
1.78-1.9290.4952.81506616571.3695.2
1.92-2.1112.530.3065.22126316661.1295.6
2.11-2.4212.870.1797.72172716690.7594.3
2.42-3.0412.940.095132160916500.6392.5
3.04-34.8912.810.03932.42171816810.4788.3

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Processing

Software
NameVersionClassificationNB
d*TREK8.0Ldata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.207 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 433 4.6 %RANDOM
Rwork0.196 ---
obs0.197 9419 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.328 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2---0.91 Å20 Å2
3---1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms514 0 0 81 595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022539
X-RAY DIFFRACTIONr_angle_refined_deg1.41.977736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.427565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78326.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0621582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.402151
X-RAY DIFFRACTIONr_chiral_restr0.0930.275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021437
X-RAY DIFFRACTIONr_mcbond_it0.7241.5326
X-RAY DIFFRACTIONr_mcangle_it1.292527
X-RAY DIFFRACTIONr_scbond_it2.1423213
X-RAY DIFFRACTIONr_scangle_it3.5334.5209
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 25 -
Rwork0.299 637 -
all-662 -
obs--89.95 %
Refinement TLS params.Method: refined / Origin x: 26.721 Å / Origin y: 13.262 Å / Origin z: 4.591 Å
111213212223313233
T-0.1788 Å20.0132 Å2-0.0006 Å2--0.1795 Å2-0.0022 Å2---0.2064 Å2
L3.6482 °2-1.1872 °21.2769 °2-3.0647 °2-1.087 °2--4.2674 °2
S0.022 Å °0.0152 Å °0.092 Å °0.0414 Å °-0.0077 Å °-0.1264 Å °-0.0487 Å °0.1627 Å °-0.0143 Å °

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