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- PDB-6y1i: Human Eg5 motor domain mutant R234C -

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Basic information

Entry
Database: PDB / ID: 6y1i
TitleHuman Eg5 motor domain mutant R234C
ComponentsKinesin-like protein KIF11
KeywordsMOTOR PROTEIN / Eg5 motor domain mutant R234C / KIF11 motor domain mutant R234C / human syndrome associated Eg5 mutant / kinesin
Function / homology
Function and homology information


spindle elongation / regulation of mitotic centrosome separation / plus-end-directed microtubule motor activity / Kinesins / mitotic centrosome separation / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / plus-end-directed microtubule motor activity / Kinesins / mitotic centrosome separation / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / spindle / spindle pole / mitotic spindle / mitotic cell cycle / microtubule binding / microtubule / ciliary basal body / cell division / intracellular membrane-bounded organelle / protein kinase binding / protein-containing complex / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / 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 / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGarcia-Saez, I. / Skoufias, D.A.
CitationJournal: To Be Published
Title: Human Eg5 motor domain mutant R234C
Authors: Garcia-Saez, I. / Skoufias, D.A.
History
DepositionFeb 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF11
B: Kinesin-like protein KIF11
C: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3599
Polymers123,0053
Non-polymers1,3556
Water00
1
A: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4533
Polymers41,0021
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4533
Polymers41,0021
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4533
Polymers41,0021
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.428, 87.603, 95.065
Angle α, β, γ (deg.)90.000, 116.820, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 16 through 52 or resid 64...
21(chain B and (resid 16 through 140 or resid 142...
31(chain C and (resid 16 through 52 or resid 64...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYVALVAL(chain A and (resid 16 through 52 or resid 64...AA16 - 5216 - 52
12LYSLYSLEULEU(chain A and (resid 16 through 52 or resid 64...AA64 - 14064 - 140
13GLNGLNGLUGLU(chain A and (resid 16 through 52 or resid 64...AA142 - 180142 - 180
14LEULEUVALVAL(chain A and (resid 16 through 52 or resid 64...AA182 - 365182 - 365
21GLYGLYLEULEU(chain B and (resid 16 through 140 or resid 142...BB16 - 14016 - 140
22GLNGLNGLUGLU(chain B and (resid 16 through 140 or resid 142...BB142 - 180142 - 180
23LEULEUGLUGLU(chain B and (resid 16 through 140 or resid 142...BB182 - 270182 - 270
24GLYGLYVALVAL(chain B and (resid 16 through 140 or resid 142...BB286 - 365286 - 365
31GLYGLYVALVAL(chain C and (resid 16 through 52 or resid 64...CC16 - 5216 - 52
32LYSLYSLEULEU(chain C and (resid 16 through 52 or resid 64...CC64 - 14064 - 140
33GLNGLNGLUGLU(chain C and (resid 16 through 52 or resid 64...CC142 - 180142 - 180
34LEULEUVALVAL(chain C and (resid 16 through 52 or resid 64...CC182 - 365182 - 365

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Components

#1: Protein Kinesin-like protein KIF11 / Kinesin-like protein 1 / Kinesin-like spindle protein HKSP / Kinesin-related motor protein Eg5 / ...Kinesin-like protein 1 / Kinesin-like spindle protein HKSP / Kinesin-related motor protein Eg5 / Thyroid receptor-interacting protein 5 / TRIP-5


Mass: 41001.531 Da / Num. of mol.: 3 / Mutation: R234C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Production host: Escherichia coli (E. coli) / References: UniProt: P52732
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG3350, 0.15M Na tartrate, 0.1M MES pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97888 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97888 Å / Relative weight: 1
ReflectionResolution: 3→47.7 Å / Num. obs: 51247 / % possible obs: 99.47 % / Redundancy: 2 % / Biso Wilson estimate: 78.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05018 / Rpim(I) all: 0.05018 / Rrim(I) all: 0.07096 / Net I/σ(I): 6.72
Reflection shellResolution: 3→3.107 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5642 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 5120 / CC1/2: 0.766 / Rpim(I) all: 0.5642 / Rrim(I) all: 0.798 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1II6

1ii6


Resolution: 3→47.7 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 38.35
Details: The structure has been solved using the space group P21 and 3 molecules/au including NCS and TLS in the refinement. However initially, crystals could be indexed as monoclinic (P21) or ...Details: The structure has been solved using the space group P21 and 3 molecules/au including NCS and TLS in the refinement. However initially, crystals could be indexed as monoclinic (P21) or centered orthorrombic (C222). Xtriage was run to analyze the data. These analyses pointed the possibility of a higher symmetry in the crystal (point group C222), however it was noted that the data could be perfectly twinned hence the symmetry will appear to be higher than it actually is. The largest off-origin peak in the Patterson function calculated is 5.55% of the height of the origin peak (fraction coordinates= 0.000, 0.203, 0.000; distance to origin= 17.754), with no significant pseudo translation detected. A twin law was also identified (h,-k,-h-l). Despite that the results of the L-test indicated that the intensities statistics behave as expected showing no twinning, the correlation between the intensities related by the twin law h,-k,-h-l with an estimated twin fraction of 0.19 (Britton analyses) indicated that most likely there is a NCS axis parallel to the twin axis. We suspect that the very high disorder observed in the subunit C of the au of the deposited structure it is associated to this problem. However including the twin laws in PHENIX refinements increase Rfree factor and worsened the density maps. The structure was also solved using a higher symmetry (C222) but Rfree factor increased with refinement possibly indicating a wrong space group.
RfactorNum. reflection% reflection
Rfree0.3065 2475 4.96 %
Rwork0.2719 --
obs0.2736 49949 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 547.69 Å2 / Biso mean: 194.7114 Å2 / Biso min: 42.11 Å2
Refinement stepCycle: final / Resolution: 3→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7607 0 120 0 7727
Biso mean--207.17 --
Num. residues----971
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2790X-RAY DIFFRACTION6.202TORSIONAL
12B2790X-RAY DIFFRACTION6.202TORSIONAL
13C2790X-RAY DIFFRACTION6.202TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.060.39281340.358926182752100
3.06-3.120.40331470.362426872834100
3.12-3.190.30971000.348826722772100
3.19-3.260.361460.339526482794100
3.26-3.340.42321580.35792613277199
3.34-3.430.36551170.34927052822100
3.43-3.540.36861390.30952639277899
3.54-3.650.35481310.30672638276999
3.65-3.780.27511400.28732641278199
3.78-3.930.3271260.29012643276999
3.93-4.110.32531810.274926052786100
4.11-4.330.31831720.259826592831100
4.33-4.60.23261670.232606277399
4.6-4.950.2821900.23792645273599
4.95-5.450.26591580.26362624278299
5.45-6.240.31561220.29622661278399
6.24-7.850.34511520.27772578273098
7.85-47.70.2306950.20972592268796

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