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- PDB-2v0o: FCHO2 F-BAR domain -

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Basic information

Entry
Database: PDB / ID: 2v0o
TitleFCHO2 F-BAR domain
ComponentsFCH DOMAIN ONLY PROTEIN 2
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / EFC DOMAIN / VESICLE TRAFFICKING / MEMBRANE CURVATURE / ENDOCYTOSIS / EXOCYTOSIS / F-BAR DOMAIN / POLYMORPHISM / LIPID- BINDING PROTEIN / COILED-COIL
Function / homology
Function and homology information


membrane invagination / clathrin coat assembly / clathrin-dependent endocytosis / clathrin-coated vesicle / phosphatidylserine binding / synaptic vesicle endocytosis / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / protein localization to plasma membrane ...membrane invagination / clathrin coat assembly / clathrin-dependent endocytosis / clathrin-coated vesicle / phosphatidylserine binding / synaptic vesicle endocytosis / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / protein localization to plasma membrane / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
F-BAR domain only protein 2 / : / GEM-interacting protein-like, FCH domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain ...F-BAR domain only protein 2 / : / GEM-interacting protein-like, FCH domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / Mu homology domain / Mu homology domain (MHD) profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / F-BAR domain only protein 2 / F-BAR domain only protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsHenne, W.M. / McMahon, H.T. / Kent, H.M. / Evans, P.R.
CitationJournal: Structure / Year: 2007
Title: Structure and Analysis of Fcho2 F-Bar Domain: A Dimerizing and Membrane Recruitment Module that Effects Membrane Curvature.
Authors: Henne, W.M. / Kent, H.M. / Ford, M.J.G. / Hedge, B.G. / Daumke, O. / Butler, P.J. / Mittal, R. / Langen, R. / Evans, P.R. / Mcmahon, H.T.
History
DepositionMay 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FCH DOMAIN ONLY PROTEIN 2
B: FCH DOMAIN ONLY PROTEIN 2
C: FCH DOMAIN ONLY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7606
Polymers94,5833
Non-polymers1773
Water3,243180
1
A: FCH DOMAIN ONLY PROTEIN 2
B: FCH DOMAIN ONLY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1744
Polymers63,0552
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: FCH DOMAIN ONLY PROTEIN 2
hetero molecules

C: FCH DOMAIN ONLY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1744
Polymers63,0552
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)254.440, 65.680, 89.910
Angle α, β, γ (deg.)90.00, 110.32, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99957, -0.02891, -0.00502), (-0.02905, 0.9991, 0.03105), (0.00412, 0.03119, -0.99951)128.64897, 1.07341, 49.14447
2given(-0.76127, 0.01968, -0.64814), (-0.00427, -0.99967, -0.02534), (-0.64843, -0.01652, 0.7611)176.01089, 27.83235, 65.42796

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Components

#1: Protein FCH DOMAIN ONLY PROTEIN 2 / FCHO2


Mass: 31527.719 Da / Num. of mol.: 3 / Fragment: F-BAR DOMAIN, RESIDUES 1-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: Q96CF5, UniProt: Q0JRZ9*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST 4 RESIDUES LGSP ARE A CLONING ARTEFACT FROM THE PLASMID

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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: 3.7 Å3/Da / Density % sol: 66.97 % / Description: 2 SIMILAR HG DERIVATIVES
Crystal growpH: 9 / Details: 18% PEG4000, 300MM NA ACETATE, 100MM TRIS PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 61810 / % possible obs: 99.5 % / Observed criterion σ(I): -10 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→119.52 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.472 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ASYMMETRIC UNIT CONTAINS 1.5 DIMERS, ONE COMPRISING CHAINS A & B, AND THE OTHER CHAIN C WHICH FORMS A DIMER WITH ITS SYMMETRY MATE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ASYMMETRIC UNIT CONTAINS 1.5 DIMERS, ONE COMPRISING CHAINS A & B, AND THE OTHER CHAIN C WHICH FORMS A DIMER WITH ITS SYMMETRY MATE RELATED BY THE SYMMETRY OPERATOR (1-X,Y,1-Z).
RfactorNum. reflection% reflectionSelection details
Rfree0.316 3140 5.1 %RANDOM
Rwork0.278 ---
obs0.28 58658 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.93 Å2
Baniso -1Baniso -2Baniso -3
1--6.45 Å20 Å2-2.42 Å2
2--0.37 Å20 Å2
3---4.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6565 0 12 180 6757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0226677
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7371.9518951
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7385813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98525.913323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.079151337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7311521
X-RAY DIFFRACTIONr_chiral_restr0.050.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024900
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1520.23151
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.280.24745
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.2108
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2411.54263
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.43426525
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.29432777
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5094.52426
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.458 228
Rwork0.41 4305

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