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- PDB-2c08: Rat endophilin A1 BAR domain -

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Basic information

Entry
Database: PDB / ID: 2c08
TitleRat endophilin A1 BAR domain
ComponentsSH3-CONTAINING GRB2-LIKE PROTEIN 2
KeywordsTRANSFERASE / ENDOCYTOSIS / BAR DOMAIN / MEMBRANE CURVATURE / SH3 DOMAIN / ACYLTRANSFERASE / COILED COIL / LIPID-BINDING / MULTIGENE FAMILY / PHOSPHORYLATION
Function / homology
Function and homology information


Negative regulation of MET activity / membrane bending / positive regulation of membrane tubulation / EGFR downregulation / lipid tube assembly / vesicle scission / membrane tubulation / regulation of clathrin-dependent endocytosis / basal dendrite / Retrograde neurotrophin signalling ...Negative regulation of MET activity / membrane bending / positive regulation of membrane tubulation / EGFR downregulation / lipid tube assembly / vesicle scission / membrane tubulation / regulation of clathrin-dependent endocytosis / basal dendrite / Retrograde neurotrophin signalling / Lysosome Vesicle Biogenesis / regulation of receptor internalization / negative regulation of blood-brain barrier permeability / synaptic vesicle uncoating / Golgi Associated Vesicle Biogenesis / dendrite extension / MHC class II antigen presentation / postsynaptic actin cytoskeleton organization / photoreceptor ribbon synapse / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynaptic cytosol / synaptic vesicle endocytosis / cellular response to brain-derived neurotrophic factor stimulus / hippocampal mossy fiber to CA3 synapse / negative regulation of protein phosphorylation / Schaffer collateral - CA1 synapse / synaptic vesicle membrane / neuron projection development / presynapse / postsynapse / transmembrane transporter binding / early endosome / negative regulation of gene expression / neuronal cell body / lipid binding / glutamatergic synapse / synapse / protein kinase binding / perinuclear region of cytoplasm / identical protein binding / plasma membrane / cytoplasm
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 / Src homology 3 domains ...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 speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsGallop, J.L. / Kent, H.M. / Mcmahon, H.T. / Evans, P.R.
CitationJournal: Embo J. / Year: 2006
Title: Mechanism of Endophilin N-Bar Domain-Mediated Membrane Curvature.
Authors: Gallop, J.L. / Jao, C.C. / Kent, H.M. / Butler, P.J. / Evans, P.R. / Langen, R. / Mcmahon, H.T.
History
DepositionAug 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 29, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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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


Theoretical massNumber of molelcules
Total (without water)24,0251
Polymers24,0251
Non-polymers00
Water0
1
A: SH3-CONTAINING GRB2-LIKE PROTEIN 2

A: SH3-CONTAINING GRB2-LIKE PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)48,0502
Polymers48,0502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.578, 126.578, 101.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein SH3-CONTAINING GRB2-LIKE PROTEIN 2 / ENDOPHILIN A1 / SH3 DOMAIN PROTEIN 2A / SH3P4


Mass: 24025.070 Da / Num. of mol.: 1 / Fragment: BAR DOMAIN, RESIDUES 1-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: O35179, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Sequence detailsUNIPROT DOES NOT CURRENTLY HAVE A FULL-LENGTH ENTRY FOR RAT ENDOPHILIN A1. THE FRAGMENTS FROM 25- ...UNIPROT DOES NOT CURRENTLY HAVE A FULL-LENGTH ENTRY FOR RAT ENDOPHILIN A1. THE FRAGMENTS FROM 25-104 HAS BEEN MAPPED TO ITSELF AT THE PRESENT TIME DUE TO A LACK OF AVAILABLE SEQUENCE DATABASE MAPPING

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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: 8.76 Å3/Da / Density % sol: 85.85 %
Crystal growTemperature: 277 K / pH: 8
Details: 25% BUTANE-1,4-DIOL, 100MM TRIS PH 8.0,4DEGC, CRYOPROTECTED IN 40% BUTANE-1,4-DIOL, 25% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 5, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→44 Å / Num. obs: 393336 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 22.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 19.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→89.44 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.861 / SU B: 12.411 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.273
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 904 5.1 %RANDOM
Rwork0.279 ---
obs0.28 16875 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.9→89.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1653 0 0 0 1653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0231820
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9561.9852234
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4615202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8125.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83615346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3251513
X-RAY DIFFRACTIONr_chiral_restr0.0720.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021242
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2708
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21169
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5951.51193
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69621629
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2393675
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8334.5605
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.338 65
Rwork0.361 1235

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