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- PDB-7s5u: Extended bipolar assembly domain of kinesin-5 minifilament -

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Basic information

Entry
Database: PDB / ID: 7s5u
TitleExtended bipolar assembly domain of kinesin-5 minifilament
ComponentsKinesin-like protein Klp61F
KeywordsCELL CYCLE / Kinesin-5 / Bipolar assembly / four-helical-bundle
Function / homology
Function and homology information


aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / spindle elongation / mitotic spindle microtubule / positive regulation of Golgi to plasma membrane protein transport ...aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / spindle elongation / mitotic spindle microtubule / positive regulation of Golgi to plasma membrane protein transport / microtubule bundle formation / plus-end-directed microtubule motor activity / mitotic centrosome separation / microtubule associated complex / kinesin complex / microtubule-based movement / mitotic spindle pole / Golgi organization / cytoskeletal motor activity / protein secretion / mitotic spindle assembly / mitotic spindle organization / spindle microtubule / mitotic spindle / spindle / mitotic cell cycle / microtubule binding / microtubule / cell division / Golgi apparatus / endoplasmic reticulum / ATP binding / nucleus / cytoplasm
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / 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-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / 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
Similarity search - Domain/homology
Kinesin-like protein Klp61F
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.41 Å
AuthorsNithianantham, S. / Al-Bassam, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110283 United States
National Science Foundation (NSF, United States)1615991 United States
CitationJournal: Mol.Biol.Cell / Year: 2023
Title: The kinesin-5 tail and bipolar miniflament domains are the origin of its microtubule crosslinking and sliding activity.
Authors: Nithianantham, S. / Iwanski, M.K. / Gaska, I. / Pandey, H. / Bodrug, T. / Inagaki, S. / Major, J. / Brouhard, G.J. / Gheber, L. / Rosenfeld, S.S. / Forth, S. / Hendricks, A.G. / Al-Bassam, J.
History
DepositionSep 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein Klp61F
B: Kinesin-like protein Klp61F
D: Kinesin-like protein Klp61F
C: Kinesin-like protein Klp61F


Theoretical massNumber of molelcules
Total (without water)113,7334
Polymers113,7334
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-111 kcal/mol
Surface area46820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)253.180, 84.890, 96.770
Angle α, β, γ (deg.)90.000, 91.440, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 623 through 631 and (name N...
21(chain B and ((resid 623 through 631 and (name N...
12(chain C and (resid 624 or (resid 626 through 640...
22(chain D and (resid 624 or (resid 626 through 640...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNGLUGLU(chain A and ((resid 623 through 631 and (name N...AA623 - 63128 - 36
121ASPASPGLYGLY(chain A and ((resid 623 through 631 and (name N...AA619 - 79724 - 202
131ASPASPGLYGLY(chain A and ((resid 623 through 631 and (name N...AA619 - 79724 - 202
141ASPASPGLYGLY(chain A and ((resid 623 through 631 and (name N...AA619 - 79724 - 202
151ASPASPGLYGLY(chain A and ((resid 623 through 631 and (name N...AA619 - 79724 - 202
211GLNGLNGLUGLU(chain B and ((resid 623 through 631 and (name N...BB623 - 63128 - 36
221SERSERLEULEU(chain B and ((resid 623 through 631 and (name N...BB622 - 80127 - 206
231SERSERLEULEU(chain B and ((resid 623 through 631 and (name N...BB622 - 80127 - 206
241SERSERLEULEU(chain B and ((resid 623 through 631 and (name N...BB622 - 80127 - 206
251SERSERLEULEU(chain B and ((resid 623 through 631 and (name N...BB622 - 80127 - 206
112ALAALAALAALA(chain C and (resid 624 or (resid 626 through 640...CD62429
122VALVALMETMET(chain C and (resid 624 or (resid 626 through 640...CD626 - 64031 - 45
132GLNGLNSERSER(chain C and (resid 624 or (resid 626 through 640...CD620 - 79225 - 197
142GLNGLNSERSER(chain C and (resid 624 or (resid 626 through 640...CD620 - 79225 - 197
152GLNGLNSERSER(chain C and (resid 624 or (resid 626 through 640...CD620 - 79225 - 197
162GLNGLNSERSER(chain C and (resid 624 or (resid 626 through 640...CD620 - 79225 - 197
212ALAALAALAALA(chain D and (resid 624 or (resid 626 through 640...DC62429
222VALVALMETMET(chain D and (resid 624 or (resid 626 through 640...DC626 - 64031 - 45
232GLNGLNSERSER(chain D and (resid 624 or (resid 626 through 640...DC623 - 79228 - 197
242GLNGLNSERSER(chain D and (resid 624 or (resid 626 through 640...DC623 - 79228 - 197
252GLNGLNSERSER(chain D and (resid 624 or (resid 626 through 640...DC623 - 79228 - 197
262GLNGLNSERSER(chain D and (resid 624 or (resid 626 through 640...DC623 - 79228 - 197

NCS ensembles :
ID
1
2

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Components

#1: Protein
Kinesin-like protein Klp61F / Bipolar kinesin KRP-130


Mass: 28433.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Klp61F, KLP2, CG9191 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46863

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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: 4.57 Å3/Da / Density % sol: 73.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.01 M FeCl3, 0.1M sodium citrate pH 5.6, 12% Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.01
ReflectionResolution: 4.4→96.74 Å / Num. obs: 13060 / % possible obs: 98.7 % / Redundancy: 4.3 % / Rpim(I) all: 0.064 / Rrim(I) all: 0.133 / Rsym value: 0.103 / Net I/av σ(I): 3.4 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
4.4-4.644.30.4731.5796418610.2920.6050.4731.898.8
4.64-4.924.10.3751.8723417850.230.4630.3752.398.1
4.92-5.264.40.242.8754016960.1550.3240.242.899.2
5.26-5.684.50.4091.8698815590.2530.5360.4091.797.9
5.68-6.224.20.7331612114490.440.9090.7331.599.4
6.22-6.964.30.3112.4569913220.190.4020.311398.9
6.96-8.034.40.1295.1516811820.0790.1680.1296.499.6
8.03-9.843.90.0637.338359860.040.0820.06310.398.4
9.84-13.914.30.0438.533377840.0260.0540.04316.299.1
13.91-96.7353.90.0438.317114360.0240.0510.04320.596.9

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PXT

4pxt


Resolution: 4.41→96.735 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 37.55 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3097 558 5.31 %
Rwork0.2741 9295 -
obs0.2767 10515 79.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 245.09 Å2 / Biso mean: 113.6147 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 4.41→96.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5023 0 0 0 5023
Num. residues----702
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A862X-RAY DIFFRACTION4.244TORSIONAL
12B862X-RAY DIFFRACTION4.244TORSIONAL
21C876X-RAY DIFFRACTION4.244TORSIONAL
22D876X-RAY DIFFRACTION4.244TORSIONAL
LS refinement shellResolution: 4.41→4.82 Å /
Rfactor% reflection
Rfree0.368 -
Rwork0.31 -
obs-47.5 %
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)
14.29681.50041.69810.67210.45310.5568-0.15890.15770.1796-0.08310.16840.0493-0.0738-0.01060.09440.6987-0.06350.11320.7757-0.21390.498334.911253.028131.7261
25.88841.36540.74710.31840.17180.0956-0.11010.3859-0.09290.0880.1326-0.3147-0.17480.524-0.05411.6091-0.079-0.13981.55920.01821.5618-68.4675.2226-25.7899
38.82010.4261-0.95373.6780.63572.09610.1497-0.2788-0.56350.0712-0.00720.17460.361-0.2788-0.09390.6387-0.1456-0.10840.795-0.080.5769-131.8783-0.4963-44.6285
44.7441.92292.20940.75270.89250.9871-0.40910.27480.3926-0.030.05730.0918-0.56490.52650.2140.8489-0.2591-0.050.9830.29190.714-80.333713.4116-29.8517
54.46641.41792.31760.73670.81581.8034-0.12190.174-0.28620.10540.0211-0.10660.2193-0.27190.05590.7022-0.39170.25021.0215-0.15350.649818.421740.459722.3951
65.26263.37523.31721.7271.95851.9465-0.3016-0.23540.3454-0.036-0.05870.2530.1372-0.22730.07970.59910.01920.12620.54950.10250.805184.423561.774946.8909
71.13070.26990.12120.53840.02870.36330.2747-0.28870.2985-0.23110.27180.46230.120.1065-0.01580.9142-0.35350.65821.2294-0.27830.2798-24.027334.7076-0.1742
83.81973.14714.03924.27122.49764.689-0.26610.13820.2119-0.1506-0.08480.1926-0.0452-0.26850.20150.7936-0.10.16380.79290.10260.1958-126.2964-9.9669-42.853
95.75512.96736.92972.03443.41068.37750.2926-0.61730.04460.293-0.205-0.07950.1185-0.1096-0.05220.85610.00250.16130.8773-0.08120.9404-98.0601-0.3759-27.4874
100.4678-0.20790.42010.1551-0.12620.5308-0.22550.0075-0.00140.11350.18290.0797-0.06610.06550.0590.7860.03560.02850.85010.02520.4112-12.795737.85739.7989
110.5586-0.1229-1.67836.12680.56255.0493-0.13730.39690.1604-0.20780.09780.0862-0.22090.0370.04291.1834-0.0675-0.03541.27310.11061.308973.008967.066235.1364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 619 through 772 )A619 - 772
2X-RAY DIFFRACTION2chain 'A' and (resid 773 through 792 )A773 - 792
3X-RAY DIFFRACTION3chain 'B' and (resid 626 through 639 )B626 - 639
4X-RAY DIFFRACTION4chain 'B' and (resid 640 through 699 )B640 - 699
5X-RAY DIFFRACTION5chain 'B' and (resid 700 through 792 )B700 - 792
6X-RAY DIFFRACTION6chain 'C' and (resid 626 through 697 )C626 - 697
7X-RAY DIFFRACTION7chain 'C' and (resid 698 through 792 )C698 - 792
8X-RAY DIFFRACTION8chain 'D' and (resid 625 through 645 )D625 - 645
9X-RAY DIFFRACTION9chain 'D' and (resid 646 through 668 )D646 - 668
10X-RAY DIFFRACTION10chain 'D' and (resid 669 through 780 )D669 - 780
11X-RAY DIFFRACTION11chain 'D' and (resid 781 through 792 )D781 - 792

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