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- PDB-5mio: KIF2C-DARPIN FUSION PROTEIN BOUND TO TUBULIN -

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Basic information

Entry
Database: PDB / ID: 5mio
TitleKIF2C-DARPIN FUSION PROTEIN BOUND TO TUBULIN
Components
  • Kinesin-like protein KIF2C,KIF2C FUSED TO A DARPIN,KIF2C FUSED TO A DARPIN
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsMOTOR PROTEIN / KINESIN-13 MICROTUBULE ATPASE MOTOR PROTEIN
Function / homology
Function and homology information


regulation of chromosome segregation / establishment or maintenance of microtubule cytoskeleton polarity / metaphase chromosome alignment / microtubule plus-end / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / Kinesins / microtubule depolymerization / COPI-dependent Golgi-to-ER retrograde traffic ...regulation of chromosome segregation / establishment or maintenance of microtubule cytoskeleton polarity / metaphase chromosome alignment / microtubule plus-end / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / Kinesins / microtubule depolymerization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / mitotic metaphase chromosome alignment / microtubule-based movement / chromosome, centromeric region / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / kinetochore / microtubule cytoskeleton organization / spindle / Separation of Sister Chromatids / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / cell division / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Helix hairpin bin / Kinesin-like protein / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain ...Helix hairpin bin / Kinesin-like protein / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / 60s Ribosomal Protein L30; Chain: A; / Kinesin motor domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix Hairpins / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-LOC / Tubulin beta chain / Tubulin alpha-1B chain / Kinesin-like protein KIF2C
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsWang, W. / Gigant, B.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0002-01 France
Fondation ARCPDF 20130606987 France
CitationJournal: Nat Commun / Year: 2017
Title: Insight into microtubule disassembly by kinesin-13s from the structure of Kif2C bound to tubulin.
Authors: Wang, W. / Cantos-Fernandes, S. / Lv, Y. / Kuerban, H. / Ahmad, S. / Wang, C. / Gigant, B.
History
DepositionNov 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_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_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Kinesin-like protein KIF2C,KIF2C FUSED TO A DARPIN,KIF2C FUSED TO A DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,2359
Polymers162,3153
Non-polymers1,9216
Water00
1
A: Tubulin alpha-1B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7523
Polymers50,2041
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8433
Polymers50,0001
Non-polymers8432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Kinesin-like protein KIF2C,KIF2C FUSED TO A DARPIN,KIF2C FUSED TO A DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6413
Polymers62,1101
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.810, 229.760, 293.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9
#3: Protein Kinesin-like protein KIF2C,KIF2C FUSED TO A DARPIN,KIF2C FUSED TO A DARPIN / Kinesin-like protein 6 / Mitotic centromere-associated kinesin / MCAK


Mass: 62110.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NECK + MOTOR DOMAIN OF KIF2C FUSED TO THE A-C2 DARPIN
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2C, KNSL6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99661

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Non-polymers , 5 types, 6 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-LOC / N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide / COLCHICINE


Mass: 399.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO6 / Comment: medication, antiinflammatory*YM
#8: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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Details

Sequence detailsFOR BETA-TUBULIN, THERE ARE THREE MAJOR ISOTYPES EXPRESSED IN THE BRAIN (BANERJEE AT AL, JBC 1988, ...FOR BETA-TUBULIN, THERE ARE THREE MAJOR ISOTYPES EXPRESSED IN THE BRAIN (BANERJEE AT AL, JBC 1988, VOL 263:3029-34). THE BETA 2B ISOTYPE SEQUENCE WAS USED BUT POINT MUTATIONS WERE INTRODUCED WHEN POSSIBLE TO TAKE THE ISOTYPE DIVERSITY INTO ACCOUNT.

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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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 40 mM Pipes-K pH 6.8 4% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.19→49 Å / Num. obs: 29646 / % possible obs: 97.3 % / Redundancy: 3.56 % / Biso Wilson estimate: 92.48 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.21 / Net I/σ(I): 5.34
Reflection shellCC1/2: 0.342 / Rrim(I) all: 2.93

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EYP, 2HEH

5eyp

2heh


Resolution: 3.19→42.91 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.874 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.666
Details: THE DEBYE AND STARANISO PROGAMS DEVELOPPED BY GLOBAL PHASING LTD. WERE APPLIED TO THE AIMLESS SCALED DATA WITHOUT TRUNCATION OF THE RESOLUTION. THESE CORRECTED ANISOTROPIC AMPLITUDES WERE ...Details: THE DEBYE AND STARANISO PROGAMS DEVELOPPED BY GLOBAL PHASING LTD. WERE APPLIED TO THE AIMLESS SCALED DATA WITHOUT TRUNCATION OF THE RESOLUTION. THESE CORRECTED ANISOTROPIC AMPLITUDES WERE USED FOR FURTHER CYCLES OF REFINEMENTS WITH BUSTER.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1009 5.07 %RANDOM
Rwork0.211 ---
obs0.213 19903 66.3 %-
Displacement parametersBiso mean: 104.06 Å2
Baniso -1Baniso -2Baniso -3
1--7.1419 Å20 Å20 Å2
2--10.4242 Å20 Å2
3----3.2823 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: 1 / Resolution: 3.19→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10299 0 122 0 10421
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110635HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114426HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3692SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes268HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1606HARMONIC5
X-RAY DIFFRACTIONt_it10635HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion18.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1393SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12613SEMIHARMONIC4
LS refinement shellResolution: 3.19→3.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.255 -5.37 %
Rwork0.244 952 -
all0.244 1006 -
obs--23.41 %
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)
11.22370.1731-0.0742.3901-0.33061.4461-0.0445-0.1454-0.376-0.09640.05140.0340.1865-0.0439-0.0070.9473-0.26360.07030.6127-0.05460.4562-24.8932-76.027431.1859
21.14960.0699-0.14143.1118-0.45132.07590.03110.0880.1076-0.38060.0734-0.0445-0.0041-0.0635-0.10451.1898-0.3130.03530.5621-0.06080.2755-14.0661-37.604216.7912
31.4017-0.3514-0.10553.4938-0.91482.4948-0.2946-0.16370.1990.15560.29090.246-0.1498-0.28390.00371.0783-0.1252-0.00560.5642-0.12030.1716-32.3371-35.311954.3047
44.1802-0.5011-1.12828.1341-3.47485.55320.03780.01420.49240.12750.0103-0.6574-0.22710.2255-0.04811.2806-0.3340.0290.6968-0.11250.53990.2437-2.107125.2663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|227:588 800:801 }
4X-RAY DIFFRACTION4{ C|622:744 }

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