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- PDB-3r7g: Crystal structure of Spire KIND domain in complex with the tail o... -

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Basic information

Entry
Database: PDB / ID: 3r7g
TitleCrystal structure of Spire KIND domain in complex with the tail of FMN2
Components
  • Formin-2Formins
  • Protein spire homolog 1
KeywordsPROTEIN BINDING / C-lobe of protein kinases / actin nucleator / Fmn-family formins
Function / homology
Function and homology information


homologous chromosome movement towards spindle pole in meiosis I anaphase / formin-nucleated actin cable assembly / establishment of meiotic spindle localization / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / Golgi vesicle transport / cleavage furrow formation / positive regulation of double-strand break repair / oogenesis ...homologous chromosome movement towards spindle pole in meiosis I anaphase / formin-nucleated actin cable assembly / establishment of meiotic spindle localization / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / Golgi vesicle transport / cleavage furrow formation / positive regulation of double-strand break repair / oogenesis / positive regulation of mitochondrial fission / microvillus / intracellular transport / vesicle-mediated transport / actin filament polymerization / cytoplasmic vesicle membrane / negative regulation of protein catabolic process / spindle / cell migration / protein transport / actin binding / cell cortex / cellular response to hypoxia / actin cytoskeleton organization / mitochondrial outer membrane / cytoskeleton / intracellular signal transduction / innate immune response / DNA damage response / endoplasmic reticulum membrane / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein Spire1 / Protein Spire / Kinase non-catalytic C-lobe domain / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. ...Protein Spire1 / Protein Spire / Kinase non-catalytic C-lobe domain / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / DEP domain / Zinc finger, FYVE/PHD-type / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein spire homolog 1 / Formin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsKreutz, B. / Vizcarra, C.L. / Rodal, A.A. / Toms, A.V. / Lu, J. / Quinlan, M.E. / Eck, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of the Spire KIND domain and insights into its interaction with Fmn-family formins
Authors: Vizcarra, C. / Kreutz, B. / Rodal, A. / Toms, A. / Lu, J. / Zheng, W. / Quinlan, M. / Eck, M.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: Protein spire homolog 1
B: Formin-2


Theoretical massNumber of molelcules
Total (without water)26,5662
Polymers26,5662
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-6 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.444, 66.444, 116.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein spire homolog 1 / Spir-1


Mass: 24027.785 Da / Num. of mol.: 1 / Fragment: KIND domain (UNP residues 20-237)
Source method: isolated from a genetically manipulated source
Details: Spir1 KIND 20-237 / Source: (gene. exp.) Homo sapiens (human) / Gene: SPIRE1, KIAA1135, SPIR1 / Plasmid: pET HisTT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q08AE8
#2: Protein/peptide Formin-2 / Formins


Mass: 2538.105 Da / Num. of mol.: 1 / Fragment: FSI domain (UNP residues 1701-1722)
Source method: isolated from a genetically manipulated source
Details: Fmn2 1700-1722 / Source: (gene. exp.) Homo sapiens (human) / Gene: FMN2 / Plasmid: pET GST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9NZ56
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6 / Details: PEG400, pH 6.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→45 Å / Num. obs: 12200 / % possible obs: 95.5 % / Rmerge(I) obs: 0.081

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
REFMAC5.5.0093refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→38.8 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.66 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22876 640 5 %RANDOM
Rwork0.19404 ---
obs0.19578 12200 92.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.877 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 0 85 1464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221408
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9671901
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6575173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93423.08868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12615258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5651516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211057
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9311.5870
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81821397
X-RAY DIFFRACTIONr_scbond_it2.6783538
X-RAY DIFFRACTIONr_scangle_it4.7214.5502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 43 -
Rwork0.326 709 -
obs--77.05 %

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