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- PDB-4ds7: Crystal structure of yeast calmodulin bound to the C-terminal fra... -

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Basic information

Entry
Database: PDB / ID: 4ds7
TitleCrystal structure of yeast calmodulin bound to the C-terminal fragment of spindle pole body protein Spc110
Components
  • Calmodulin
  • Spindle pole body component 110
KeywordsPROTEIN BINDING / METAL BINDING / SPINDLE POLE BODY / STRUCTURAL PROTEIN
Function / homology
Function and homology information


gamma-tubulin complex localization to nuclear side of mitotic spindle pole body / protein localization to mitotic spindle pole body / inner plaque of spindle pole body / central plaque of spindle pole body / regulation of microtubule nucleation / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / positive regulation of microtubule nucleation / myosin II complex / structural constituent of cytoskeleton ...gamma-tubulin complex localization to nuclear side of mitotic spindle pole body / protein localization to mitotic spindle pole body / inner plaque of spindle pole body / central plaque of spindle pole body / regulation of microtubule nucleation / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / positive regulation of microtubule nucleation / myosin II complex / structural constituent of cytoskeleton / protein-containing complex assembly / cytoskeleton / calmodulin binding / calcium ion binding / protein-containing complex binding / nucleus / cytoplasm
Similarity search - Function
Rhopdopsin 7-helix transmembrane proteins / Rhopdopsin 7-helix transmembrane proteins - #10 / Spindle pole body component 110, C-terminal / Spindle pole body component 110 C-terminal domain / EF hand / : / EF-hand / Recoverin; domain 1 / Helix non-globular / EF-hand domain pair ...Rhopdopsin 7-helix transmembrane proteins / Rhopdopsin 7-helix transmembrane proteins - #10 / Spindle pole body component 110, C-terminal / Spindle pole body component 110 C-terminal domain / EF hand / : / EF-hand / Recoverin; domain 1 / Helix non-globular / EF-hand domain pair / EF-hand, calcium binding motif / Special / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
STRONTIUM ION / Calmodulin / Spindle pole body component 110
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsKlenchin, V.A. / Rayment, I.
CitationJournal: Mol.Biol.Cell / Year: 2017
Title: The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling.
Authors: Viswanath, S. / Bonomi, M. / Kim, S.J. / Klenchin, V.A. / Taylor, K.C. / Yabut, K.C. / Umbreit, N.T. / Van Epps, H.A. / Meehl, J. / Jones, M.H. / Russel, D. / Velazquez-Muriel, J.A. / Winey, ...Authors: Viswanath, S. / Bonomi, M. / Kim, S.J. / Klenchin, V.A. / Taylor, K.C. / Yabut, K.C. / Umbreit, N.T. / Van Epps, H.A. / Meehl, J. / Jones, M.H. / Russel, D. / Velazquez-Muriel, J.A. / Winey, M. / Rayment, I. / Davis, T.N. / Sali, A. / Muller, E.G.
History
DepositionFeb 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Calmodulin
C: Calmodulin
D: Calmodulin
E: Spindle pole body component 110
F: Spindle pole body component 110
G: Spindle pole body component 110
H: Spindle pole body component 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,88421
Polymers90,7198
Non-polymers1,16513
Water4,684260
1
A: Calmodulin
F: Spindle pole body component 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0436
Polymers22,6802
Non-polymers3634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-20 kcal/mol
Surface area11980 Å2
MethodPISA
2
B: Calmodulin
E: Spindle pole body component 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1317
Polymers22,6802
Non-polymers4525
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-21 kcal/mol
Surface area12900 Å2
MethodPISA
3
C: Calmodulin
D: Calmodulin
G: Spindle pole body component 110
H: Spindle pole body component 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7108
Polymers45,3594
Non-polymers3504
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-90 kcal/mol
Surface area18390 Å2
MethodPISA
4
C: Calmodulin
G: Spindle pole body component 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8554
Polymers22,6802
Non-polymers1752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-23 kcal/mol
Surface area11790 Å2
MethodPISA
5
D: Calmodulin
H: Spindle pole body component 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8554
Polymers22,6802
Non-polymers1752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-19 kcal/mol
Surface area12370 Å2
MethodPISA
6
A: Calmodulin
B: Calmodulin
E: Spindle pole body component 110
F: Spindle pole body component 110
hetero molecules

A: Calmodulin
B: Calmodulin
E: Spindle pole body component 110
F: Spindle pole body component 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,34826
Polymers90,7198
Non-polymers1,63018
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area21440 Å2
ΔGint-193 kcal/mol
Surface area36290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.670, 145.444, 49.837
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
Calmodulin / CaM


Mass: 16076.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: CMD1, KLLA0B09427g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60041
#2: Protein
Spindle pole body component 110 / Extragenic suppressor of CMD1-1 mutant protein 1 / Nuclear filament-related protein 1 / Spindle ...Extragenic suppressor of CMD1-1 mutant protein 1 / Nuclear filament-related protein 1 / Spindle pole body spacer protein SPC110


Mass: 6602.755 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: SPC110, NUF1, XCM1, YDR356W, D9476.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32380

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Non-polymers , 4 types, 273 molecules

#3: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Sr
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 0.1M sodium acetate, 0.7M ammonium sulfate, 0.5M guanidine chloride, 0.001M strontium chloride, 0.00005M copper chloride, pH 4.5, 0.0005M LAURYLDIMETHYLAMINE OXIDE, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97153 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97153 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 47122 / Num. obs: 47075 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.9 % / Biso Wilson estimate: 41.57 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.163 / Net I/σ(I): 31.184
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.1911.73.87623210.871199.5
2.19-2.2313.24.93722930.873199.9
2.23-2.2714.26.34523410.893199.8
2.27-2.3215.57.73522830.8671100
2.32-2.3715.78.88123530.868199.9
2.37-2.4215.910.0823080.8691100
2.42-2.481611.19523220.8711100
2.48-2.5516.213.04623330.8731100
2.55-2.6216.316.05323490.9041100
2.62-2.7116.519.36122980.9131100
2.71-2.8116.621.46223550.9461100
2.81-2.9216.724.76423560.9711100
2.92-3.0516.931.36523261.0261100
3.05-3.211738.65123521.0791100
3.21-3.4117.246.98323661.1461100
3.41-3.6717.357.7323621.2891100
3.67-4.0417.269.48723851.6671100
4.04-4.6316.777.81424082.3321100
4.63-5.8216.173.03524182.091199.9
5.82-3015.780.89425461.527198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.33 Å29.72 Å
Translation2.33 Å29.72 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
d*TREKdata scaling
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HR4

3hr4


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.1932 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8427 / SU B: 8.756 / SU ML: 0.125 / SU R Cruickshank DPI: 0.2338 / SU Rfree: 0.1932 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 2346 5.1 %RANDOM
Rwork0.197 ---
all0.1992 46323 --
obs0.1992 46203 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.16 Å2 / Biso mean: 44.8885 Å2 / Biso min: 15.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---0.41 Å20 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5629 0 37 260 5926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225706
X-RAY DIFFRACTIONr_angle_refined_deg0.9841.987664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2625727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95325.249261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.982151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2851535
X-RAY DIFFRACTIONr_chiral_restr0.0680.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024179
X-RAY DIFFRACTIONr_mcbond_it1.74533647
X-RAY DIFFRACTIONr_mcangle_it3.439305790
X-RAY DIFFRACTIONr_scbond_it4.03152059
X-RAY DIFFRACTIONr_scangle_it6.677501874
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 184 -
Rwork0.206 3153 -
all-3337 -
obs--99.61 %
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)
12.43770.091-0.13675.03511.35520.95560.12270.0389-0.01370.1628-0.0350.1114-0.0859-0.0902-0.08770.03680.01690.02750.01940.0190.0287-14.58553.68420.115
22.82570.3379-0.01191.8281-0.72370.73180.154-0.2366-0.09770.0861-0.0590.1686-0.05430.0507-0.0950.0125-0.01630.00290.02350.00310.022716.39954.42421.124
31.60370.58150.31911.1840.54291.0160.0824-0.111-0.06570.02250.0633-0.12870.11660.0174-0.14570.0221-0.0017-0.01910.0268-0.01290.0298-16.78416.9744.028
44.0481-1.27840.65536.3486-1.12141.47370.04630.35610.288-0.0612-0.0668-0.22920.01050.2250.02050.03430.00410.0360.05650.01840.055113.64920.2311.221
50.7911.54752.06553.93286.008811.61580.1799-0.1353-0.04140.2308-0.0565-0.02580.12230.0995-0.12340.1004-0.0488-0.02050.07340.0220.0566-10.34858.82231.627
61.9107-2.27892.9854.2265-5.834510.43910.30990.1979-0.1167-0.2934-0.05170.13460.1311-0.1033-0.25820.10220.0416-0.02650.0867-0.01890.047310.89760.9437.822
71.62520.96970.43964.4637-5.843111.37840.3411-0.32170.06180.43010.1140.0981-0.2327-0.6453-0.45510.1567-0.00910.02680.12270.00440.130310.06713.87913.864
80.71280.19522.04613.5024.459610.30940.05860.1561-0.0867-0.15660.28-0.1546-0.09670.6879-0.33850.0680.0055-0.0520.108-0.09570.131-13.15614.637-3.291
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B5 - 79
2X-RAY DIFFRACTION1A80 - 147
3X-RAY DIFFRACTION2A4 - 79
4X-RAY DIFFRACTION2B80 - 146
5X-RAY DIFFRACTION3D5 - 79
6X-RAY DIFFRACTION3C80 - 147
7X-RAY DIFFRACTION4C5 - 79
8X-RAY DIFFRACTION4D80 - 147
9X-RAY DIFFRACTION5E898 - 944
10X-RAY DIFFRACTION6F898 - 936
11X-RAY DIFFRACTION7G899 - 934
12X-RAY DIFFRACTION8H898 - 944

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