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- PDB-6bbn: Crystal structure of a curved tubulin complex induced by the kine... -

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Basic information

Entry
Database: PDB / ID: 6bbn
TitleCrystal structure of a curved tubulin complex induced by the kinesin-13 Kif2A
Components
  • DARPin
  • Kinesin-like protein KIF2A
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsMOTOR PROTEIN / Kinesin / Kif2A / microtubules / tubulin / kinesin-13
Function / homology
Function and homology information


centriolar subdistal appendage / Kinesins / positive regulation of axon guidance / kinesin complex / microtubule depolymerization / microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / cytoskeletal motor activity / mitotic spindle assembly ...centriolar subdistal appendage / Kinesins / positive regulation of axon guidance / kinesin complex / microtubule depolymerization / microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / cytoskeletal motor activity / mitotic spindle assembly / microtubule-based process / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / MHC class II antigen presentation / cellular response to interleukin-4 / regulation of cell migration / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / RHO GTPases Activate Formins / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / neuron migration / spindle pole / mitotic spindle / Separation of Sister Chromatids / nervous system development / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cell differentiation / nuclear body / cilium / ciliary basal body / protein heterodimerization activity / cell division / GTPase activity / ubiquitin protein ligase binding / centrosome / GTP binding / nucleolus / ATP hydrolysis activity / nucleoplasm / ATP binding / metal ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
: / Kinesin-like protein KIF2A-like, N-terminal / Kinesin motor domain / Kinesin / Kinesin-like protein / Helix hairpin bin / Ankyrin repeat-containing domain / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Kinesin motor domain signature. ...: / Kinesin-like protein KIF2A-like, N-terminal / Kinesin motor domain / Kinesin / Kinesin-like protein / Helix hairpin bin / Ankyrin repeat-containing domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Helix Hairpins / Alpha Horseshoe / 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 / PHOSPHATE ION / Kinesin-like protein KIF2A / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.514 Å
AuthorsAllingham, J.S. / Trofimova, D.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat Commun / Year: 2018
Title: Ternary complex of Kif2A-bound tandem tubulin heterodimers represents a kinesin-13-mediated microtubule depolymerization reaction intermediate.
Authors: Trofimova, D. / Paydar, M. / Zara, A. / Talje, L. / Kwok, B.H. / Allingham, J.S.
History
DepositionOct 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
P: DARPin
E: Kinesin-like protein KIF2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,87016
Polymers266,2396
Non-polymers2,63110
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19080 Å2
ΔGint-125 kcal/mol
Surface area83340 Å2
Unit cell
Length a, b, c (Å)145.052, 82.188, 147.658
Angle α, β, γ (deg.)90.000, 109.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 6 molecules ACBDPE

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


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


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856
#3: Protein DARPin


Mass: 17911.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#4: Protein Kinesin-like protein KIF2A / Kinesin-2 / hK2


Mass: 47918.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2A, KIF2, KNS2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00139

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Non-polymers , 5 types, 10 molecules

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


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.57 % / Description: thin plates
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 8% PEG8000, 6% ethylene glycol, 10 mM DDT, 100 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.46→50 Å / Num. obs: 40041 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 129.71 Å2 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.131 / Rrim(I) all: 0.249 / Χ2: 1.303 / Net I/σ(I): 4.5 / Num. measured all: 142449
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.46-3.583.12.23538690.2121.4692.6851.09496.9
3.58-3.733.22.08439280.5421.3282.4791.04398
3.73-3.93.31.86239570.5251.182.2111.23898.9
3.9-4.13.51.30539780.6750.8091.5391.13199.8
4.1-4.363.70.72439770.8160.4390.8491.23499.8
4.36-4.73.80.44140550.920.2630.5141.267100
4.7-5.173.80.33340030.9480.1980.3881.291100
5.17-5.913.80.29840390.9540.1770.3471.267100
5.91-7.453.80.14940840.9850.0890.1741.417100
7.45-503.60.04141510.9980.0250.0491.91999.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4LNU & 2GRY

4lnu

2gry


Resolution: 3.514→49.217 Å / SU ML: 0.7 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2874 1945 4.92 %RANDOM
Rwork0.2363 37607 --
obs0.2391 39552 95.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 263.18 Å2 / Biso mean: 146.2432 Å2 / Biso min: 68.05 Å2
Refinement stepCycle: final / Resolution: 3.514→49.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17627 0 160 0 17787
Biso mean--135.16 --
Num. residues----2267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418159
X-RAY DIFFRACTIONf_angle_d0.68924646
X-RAY DIFFRACTIONf_chiral_restr0.0442739
X-RAY DIFFRACTIONf_plane_restr0.0053208
X-RAY DIFFRACTIONf_dihedral_angle_d6.1511595
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5136-3.60140.4983800.41621541162155
3.6014-3.69880.42031180.42272644276295
3.6988-3.80760.3881440.36622683282797
3.8076-3.93040.42341230.38482666278994
3.9304-4.07080.35651400.33772731287199
4.0708-4.23370.3181400.32832774291499
4.2337-4.42630.33951460.296427822928100
4.4263-4.65950.31481250.262128182943100
4.6595-4.95120.33551460.245828162962100
4.9512-5.3330.28481630.245827742937100
5.333-5.8690.28711690.252828172986100
5.869-6.71640.33791350.247128292964100
6.7164-8.45490.23121330.192928572990100
8.4549-49.22220.22141830.13252875305899

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