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- PDB-2d4c: Crystal structure of the endophilin BAR domain mutant -

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Basic information

Entry
Database: PDB / ID: 2d4c
TitleCrystal structure of the endophilin BAR domain mutant
ComponentsSH3-containing GRB2-like protein 2
KeywordsTRANSFERASE / BAR domain
Function / homology
Function and homology information


negative regulation of blood-brain barrier permeability / synaptic vesicle uncoating / dendrite extension / Retrograde neurotrophin signalling / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Recycling pathway of L1 / cellular response to brain-derived neurotrophic factor stimulus / MHC class II antigen presentation / InlB-mediated entry of Listeria monocytogenes into host cell ...negative regulation of blood-brain barrier permeability / synaptic vesicle uncoating / dendrite extension / Retrograde neurotrophin signalling / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Recycling pathway of L1 / cellular response to brain-derived neurotrophic factor stimulus / MHC class II antigen presentation / InlB-mediated entry of Listeria monocytogenes into host cell / negative regulation of protein phosphorylation / central nervous system development / cell projection / EGFR downregulation / clathrin-coated endocytic vesicle membrane / Negative regulation of MET activity / neuron projection development / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / early endosome / Golgi membrane / negative regulation of gene expression / lipid binding / glutamatergic synapse / perinuclear region of cytoplasm / signal transduction / identical protein binding / plasma membrane / cytosol / 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 / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / 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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMasuda, M. / Takeda, S.
CitationJournal: Embo J. / Year: 2006
Title: Endophilin BAR domain drives membrane curvature by two newly identified structure-based mechanisms
Authors: Masuda, M. / Takeda, S. / Sone, M. / Ohki, T. / Mori, H. / Kamioka, Y. / Mochizuki, N.
History
DepositionOct 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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.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_ref_seq_dif.details / _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: SH3-containing GRB2-like protein 2
B: SH3-containing GRB2-like protein 2
C: SH3-containing GRB2-like protein 2
D: SH3-containing GRB2-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2655
Polymers116,2254
Non-polymers401
Water3,549197
1
A: SH3-containing GRB2-like protein 2
B: SH3-containing GRB2-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1533
Polymers58,1122
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-51 kcal/mol
Surface area23620 Å2
MethodPISA
2
C: SH3-containing GRB2-like protein 2
D: SH3-containing GRB2-like protein 2


Theoretical massNumber of molelcules
Total (without water)58,1122
Polymers58,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-53 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.344, 212.217, 54.317
Angle α, β, γ (deg.)90.00, 96.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SH3-containing GRB2-like protein 2 / SH3 domain protein 2A / Endophilin 1 / EEN-B1


Mass: 29056.242 Da / Num. of mol.: 4 / Fragment: endophilin A1 BAR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6p3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL10-Gold
References: UniProt: Q99962, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 100mM HEPES, 200mM calcium acetate, 10mM DTT, 20% PEG3350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 38763 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.323 / Num. unique all: 3673 / % possible all: 93.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1X03

1x03


Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1919 -random
Rwork0.215 ---
all0.217 38778 --
obs0.217 38523 99.3 %-
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7204 0 1 197 7402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0051
X-RAY DIFFRACTIONc_angle_d0.9589
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.338 179 -
Rwork0.27 --
obs-3673 93.5 %

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