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- PDB-1bb9: CRYSTAL STRUCTURE OF THE SH3 DOMAIN FROM RAT AMPHIPHYSIN 2 -

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Basic information

Entry
Database: PDB / ID: 1bb9
TitleCRYSTAL STRUCTURE OF THE SH3 DOMAIN FROM RAT AMPHIPHYSIN 2
ComponentsAMPHIPHYSIN 2
KeywordsTRANSFERASE / SH3 DOMAIN
Function / homology
Function and homology information


regulation of cell cycle => GO:0051726 / lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube assembly / T-tubule organization / muscle cell differentiation / negative regulation of potassium ion transmembrane transport / varicosity ...regulation of cell cycle => GO:0051726 / lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube assembly / T-tubule organization / muscle cell differentiation / negative regulation of potassium ion transmembrane transport / varicosity / extrinsic component of synaptic vesicle membrane / axon initial segment / cerebellar mossy fiber / positive regulation of astrocyte differentiation / Clathrin-mediated endocytosis / nucleus localization / node of Ranvier / aspartic-type endopeptidase inhibitor activity / I band / RNA polymerase binding / nucleus organization / regulation of neuron differentiation / endosome to lysosome transport / negative regulation of amyloid-beta formation / positive regulation of endocytosis / positive regulation of actin filament polymerization / regulation of heart rate by cardiac conduction / synaptic vesicle endocytosis / axon terminus / T-tubule / phospholipid binding / tau protein binding / Z disc / positive regulation of GTPase activity / actin filament binding / synaptic vesicle / GTPase binding / nuclear envelope / protein-folding chaperone binding / protease binding / microtubule / endosome / positive regulation of apoptotic process / axon / glutamatergic synapse / synapse / protein-containing complex binding / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains ...Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Myc box-dependent-interacting protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.2 Å
AuthorsOwen, D.J. / Mcmahon, H.T. / Evans, P.R.
CitationJournal: EMBO J. / Year: 1998
Title: Crystal structure of the amphiphysin-2 SH3 domain and its role in the prevention of dynamin ring formation.
Authors: Owen, D.J. / Wigge, P. / Vallis, Y. / Moore, J.D. / Evans, P.R. / McMahon, H.T.
History
DepositionApr 29, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMPHIPHYSIN 2


Theoretical massNumber of molelcules
Total (without water)12,8791
Polymers12,8791
Non-polymers00
Water1,08160
1
A: AMPHIPHYSIN 2

A: AMPHIPHYSIN 2


Theoretical massNumber of molelcules
Total (without water)25,7582
Polymers25,7582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)72.140, 72.140, 34.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein AMPHIPHYSIN 2 /


Mass: 12879.215 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O08839
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS IS THE SH3 DOMAIN AT THE C-TERMINUS OF AMPHIPHYSIN-2. THIS DOMAIN BINDS TO THE PROLINE-RICH C- ...THIS IS THE SH3 DOMAIN AT THE C-TERMINUS OF AMPHIPHYSIN-2. THIS DOMAIN BINDS TO THE PROLINE-RICH C-TERMINAL DOMAIN OF DYNAMIN, AND DISSOCIATES DYNAMIN RINGS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.95 %
Description: NATIVE DATA WERE MERGED FROM 2 CRYSTALS, ONE SET TO 2.2 ANGSTROM RESOLUTION COLLECTED ON THE SRS SYNCHROTRON PX9.5, THE OTHER COLLECTED TO 3.5 ANGSTROMS WAS COLLECTED ON A ROTATING ANODE.
Crystal growMethod: vapor diffusion / pH: 6
Details: VAPOUR DIFFUSION, PROTEIN 30MG/ML, RESERVOIR 2.0M AMMONIUM SULFATE, 100MM NA CITRATE PH6.0, PLUS 2MM DTT., vapor diffusion
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
22.0 Mammonium sulfate1reservoir
3100 mMsodium citrate1reservoir
42 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→36 Å / Num. obs: 5401 / % possible obs: 99 % / Observed criterion σ(I): 6 / Redundancy: 4.2 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 4.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.201 / % possible all: 99
Reflection
*PLUS
% possible obs: 99.2 %
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIR / Resolution: 2.2→36 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 517 10 %RANDOM
Rwork0.186 ---
obs-5394 99.1 %-
Displacement parametersBiso mean: 39 Å2
Refine analyzeLuzzati sigma a obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms685 0 0 60 745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.1263
X-RAY DIFFRACTIONp_mcangle_it4.7845
X-RAY DIFFRACTIONp_scbond_it4.574
X-RAY DIFFRACTIONp_scangle_it6.7576
X-RAY DIFFRACTIONp_plane_restr0.0230.02
X-RAY DIFFRACTIONp_chiral_restr0.1230.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1780.3
X-RAY DIFFRACTIONp_planar_tor4.87
X-RAY DIFFRACTIONp_staggered_tor19.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rfree: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS

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