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- PDB-2yle: Crystal structure of the human Spir-1 KIND FSI domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 2yle
TitleCrystal structure of the human Spir-1 KIND FSI domain in complex with the FSI peptide
Components
  • FORMIN-2Formins
  • PROTEIN SPIRE HOMOLOG 1
KeywordsACTIN-BINDING PROTEIN / ACTIN POLYMERIZATION
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 / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZeth, K. / Pechlivanis, M. / Vonrhein, C. / Kerkhoff, E.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular Basis of Actin Nucleation Factor Cooperativity: Crystal Structure of the Spir-1 Kinase Non-Catalytic C-Lobe Domain (Kind)Formin-2 Formin Spir Interaction Motif (Fsi) Complex.
Authors: Zeth, K. / Pechlivanis, M. / Samol, A. / Pleiser, S. / Vonrhein, C. / Kerkhoff, E.
History
DepositionJun 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)29,1802
Polymers29,1802
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-5.8 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.675, 65.675, 77.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEIN SPIRE HOMOLOG 1 / SPIR-1 / HUMAN SPIR-1 KIND


Mass: 25838.787 Da / Num. of mol.: 1 / Fragment: HUMAN SPIR-1 DOMAIN (KIND), RESIDUES 36-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q08AE8
#2: Protein/peptide FORMIN-2 / Formins / FMN2 PROTEIN


Mass: 3341.113 Da / Num. of mol.: 1 / Fragment: 29 RESIDUE C-TERMINAL PEPTIDE, RESIDUES 1694-1722 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9NZ56
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.14 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→28 Å / Num. obs: 16921 / % possible obs: 96.2 % / Observed criterion σ(I): 2.3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 1.8→1.92 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.3 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→28.44 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.19 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST EIGHT RESIDUES OF THE PEPTIDE WERE NOT OBSERVED OWING TO DISORDER.
RfactorNum. reflection% reflectionSelection details
Rfree0.23577 891 5 %RANDOM
Rwork0.18651 ---
obs0.18884 16921 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.059 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å20 Å2
2---0.53 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 0 90 1602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221560
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9662110
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9595196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54122.77872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41215283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4131517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211167
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_it0.831.5969
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52921556
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1033591
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5094.5550
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 65 -
Rwork0.231 1231 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8076-3.9678-0.04286.36283.21674.8876-0.1792-0.5172-0.03130.24970.1610.09710.0609-0.13380.01820.00890.0171-0.00790.2347-0.00610.035627.19827.65230.747
22.4225-0.4510.32890.10390.11020.78360.0625-0.1425-0.2213-0.054-0.03640.00660.0557-0.0826-0.02610.05370.00990.00060.09530.01190.088919.68824.49417.543
32.0441-0.11610.27630.48260.20290.50960.0360.07360.2598-0.0308-0.04480.0013-0.0679-0.10050.00880.03860.02020.01240.07740.01690.083417.27936.24112.781
40.7142-0.19442.78790.5646-1.844212.7670.0632-0.02910.03080.0583-0.0197-0.0212-0.05670.0168-0.04350.0447-0.00610.01070.10510.00470.082833.68727.54925.164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 50
2X-RAY DIFFRACTION2A51 - 116
3X-RAY DIFFRACTION3A117 - 214
4X-RAY DIFFRACTION4A215 - 236

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