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- PDB-2d68: Structure of the N-terminal domain of FOP (FGFR1OP) protein -

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Basic information

Entry
Database: PDB / ID: 2d68
TitleStructure of the N-terminal domain of FOP (FGFR1OP) protein
ComponentsFOP
KeywordsCELL CYCLE / alpha helical bundle / dimer
Function / homology
Function and homology information


ciliary basal body-plasma membrane docking / microtubule anchoring / protein tyrosine kinase inhibitor activity / Signaling by cytosolic FGFR1 fusion mutants / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of G2/M transition of mitotic cell cycle ...ciliary basal body-plasma membrane docking / microtubule anchoring / protein tyrosine kinase inhibitor activity / Signaling by cytosolic FGFR1 fusion mutants / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of G2/M transition of mitotic cell cycle / centriole / Signaling by FGFR1 in disease / AURKA Activation by TPX2 / cell projection / negative regulation of protein kinase activity / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of cell growth / positive regulation of cell migration / centrosome / positive regulation of cell population proliferation / protein kinase binding / perinuclear region of cytoplasm / protein homodimerization activity / nucleus / cytosol
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #40 / FGFR1 oncogene partner (FOP), N-terminal dimerisation domain / FOP N terminal dimerisation domain / Mitochondrial Import Receptor Subunit Tom20; Chain A / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Centrosomal protein 43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsMikolajka, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of the N-terminal Domain of the FOP (FGFR1OP) Protein and Implications for its Dimerization and Centrosomal Localization.
Authors: Mikolajka, A. / Yan, X. / Popowicz, G.M. / Smialowski, P. / Nigg, E.A. / Holak, T.A.
History
DepositionNov 10, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FOP
B: FOP


Theoretical massNumber of molelcules
Total (without water)18,3092
Polymers18,3092
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-31 kcal/mol
Surface area8160 Å2
MethodPISA
2
A: FOP
B: FOP

A: FOP
B: FOP


Theoretical massNumber of molelcules
Total (without water)36,6184
Polymers36,6184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6910 Å2
ΔGint-79 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.840, 92.180, 37.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer.

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Components

#1: Protein FOP / FGFR1OP


Mass: 9154.504 Da / Num. of mol.: 2 / Fragment: residues 54-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET46 Ek\Lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3, B834 DE3 / References: UniProt: O95684
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2344.94
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop7.50,2M NaCl; 0,1M HEPES ph 7,5, 25% w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2772vapor diffusion, sitting drop7.50,2 M NaCl, 0,1M HEPES, 25% w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMPG/DESY, HAMBURG BW611.05
SYNCHROTRONMPG/DESY, HAMBURG BW620.9793 0.9796 0.9500
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMar 16, 2005
MARRESEARCH2CCDJul 6, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) double-crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.051
20.97931
30.97961
40.951
ReflectionResolution: 1.6→46.08 Å / Num. obs: 21205 / % possible obs: 94 % / Observed criterion σ(F): 2
Reflection shellResolution: 1.6→1.7 Å / % possible all: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.594 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24719 1142 5.1 %RANDOM
Rwork0.20535 ---
all0.20745 20919 --
obs0.20745 20919 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.128 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--0.69 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 0 200 1399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221216
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9831644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.995149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81324.23759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80715212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5291510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02914
X-RAY DIFFRACTIONr_nbd_refined0.2110.2589
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.216
X-RAY DIFFRACTIONr_mcbond_it0.8111.5768
X-RAY DIFFRACTIONr_mcangle_it1.34321201
X-RAY DIFFRACTIONr_scbond_it2.23494
X-RAY DIFFRACTIONr_scangle_it3.4214.5443
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 107 -
Rwork0.219 1496 -
obs--100 %

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