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- PDB-3u06: Crystal structure of the kinesin-14 NcdG347D -

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Basic information

Entry
Database: PDB / ID: 3u06
TitleCrystal structure of the kinesin-14 NcdG347D
ComponentsProtein claret segregational
KeywordsMOTOR PROTEIN / motor domain / stalk rotation / power stroke / kinesin-14 / microtubule binding / Ncd / transport / molecular motor / cell division / ATP binding / microtubules
Function / homology
Function and homology information


minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / spindle assembly involved in female meiosis / regulation of mitotic spindle assembly / minus-end-directed microtubule motor activity ...minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / spindle assembly involved in female meiosis / regulation of mitotic spindle assembly / minus-end-directed microtubule motor activity / microtubule bundle formation / meiotic spindle / mitotic centrosome separation / spindle organization / mitotic spindle assembly / mRNA transport / mitotic spindle organization / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / spindle / microtubule binding / hydrolase activity / cell division / centrosome / protein homodimerization activity / ATP binding / nucleus / cytosol
Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein claret segregational
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsLiu, H.-L. / Pemble IV, C.W. / Endow, S.A.
CitationJournal: Sci Rep / Year: 2012
Title: Neck-motor interactions trigger rotation of the kinesin stalk.
Authors: Liu, H.L. / Pemble Iv, C.W. / Endow, S.A.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein claret segregational
B: Protein claret segregational
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,92110
Polymers93,5822
Non-polymers1,3398
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-52 kcal/mol
Surface area34820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.539, 67.094, 94.369
Angle α, β, γ (deg.)90.000, 98.910, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein claret segregational


Mass: 46790.789 Da / Num. of mol.: 2 / Fragment: unp residues 293-700
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CA(ND), CG7831, ncd, non-claret disjunctional / Plasmid: pMW172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20480
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Bis-Tris propane, Na2SO4, PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2011
RadiationMonochromator: double crystal (22-ID line) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 41863 / Num. obs: 36362 / % possible obs: 86.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.072 / Χ2: 1.114 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.35-2.394.10.4251.9212290.87459.3
2.39-2.434.60.3862.4712370.88659.9
2.43-2.4850.3673.0912630.8160.1
2.48-2.535.10.343.4113420.95265.3
2.53-2.595.30.3383.4514550.89669
2.59-2.655.60.2924.315350.93974.4
2.65-2.715.70.294.3616430.92279.1
2.71-2.795.80.2425.2117800.91185.1
2.79-2.875.90.2086.4518700.97390.7
2.87-2.9660.1847.9119740.98194.8
2.96-3.076.20.1719.3920581.02298.2
3.07-3.196.30.14711.6520621.04199.7
3.19-3.336.40.1215.521161.16100
3.33-3.516.40.09820.7921041.319100
3.51-3.736.30.07528.2720791.444100
3.73-4.026.40.06136.0520891.456100
4.02-4.426.40.04844.2321061.39100
4.42-5.066.30.03949.621151.243100
5.06-6.376.30.03845.2421151.092100
6.37-5060.02954.6221901.109100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.2_868refinement
PDB_EXTRACT3.1data extraction
SERGUI(APS)data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.615 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.56 / σ(F): 2 / σ(I): 2 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 1817 5 %random
Rwork0.2157 ---
obs0.2174 36329 86.14 %-
all-41863 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.912 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 171.04 Å2 / Biso mean: 70.9931 Å2 / Biso min: 25.76 Å2
Baniso -1Baniso -2Baniso -3
1-6.1308 Å2-0 Å219.6033 Å2
2---2.0237 Å20 Å2
3----4.1071 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5624 0 85 122 5831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045809
X-RAY DIFFRACTIONf_angle_d0.7597843
X-RAY DIFFRACTIONf_chiral_restr0.045881
X-RAY DIFFRACTIONf_plane_restr0.0031003
X-RAY DIFFRACTIONf_dihedral_angle_d16.9922197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3387-2.4020.32671000.29981582168253
2.402-2.47260.32051130.26911814192759
2.4726-2.55240.28621090.26071997210666
2.5524-2.64370.28861220.25012245236773
2.6437-2.74950.30141380.24942481261982
2.7495-2.87460.26511550.24312763291890
2.8746-3.02610.27031450.23292967311297
3.0261-3.21570.2551620.231230853247100
3.2157-3.46390.25991350.219430773212100
3.4639-3.81240.21541480.20331113259100
3.8124-4.36370.22261490.190330983247100
4.3637-5.49640.23251770.187931063283100
5.4964-46.62380.25461640.219831863350100
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)
10.08470.2765-0.52740.33930.05740.2593-0.2082-0.0657-0.5745-0.1418-0.1126-0.24260.1130.1256-0.00010.3026-0.02330.01010.40070.07880.391331.9527-4.32827.8874
21.1030.24310.05450.9771-0.38581.37740.0243-0.09910.05830.12840.05750.1396-0.2491-0.21510.00010.37350.03990.05070.25960.01340.3165-7.73185.501922.7379
30.63770.6352-0.64390.2037-0.89410.40240.1348-0.07390.0767-0.1363-0.126-0.064-0.08810.2075-00.3718-0.01410.01340.3924-0.00680.439825.2887-16.181213.206
41.1081-0.02320.07251.5319-0.18881.4597-0.0968-0.656-0.11010.32310.1053-0.02810.19610.1451-0.00870.32560.0983-0.12090.64960.01010.360319.1138-31.182138.5891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 292:346)A292 - 346
2X-RAY DIFFRACTION2chain 'A' and (resseq 347:672)A347 - 672
3X-RAY DIFFRACTION3chain 'B' and (resseq 290:402)B290 - 402
4X-RAY DIFFRACTION4chain 'B' and (resseq 403:673)B403 - 673

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