[English] 日本語
Yorodumi
- PDB-6bbn: Crystal structure of a curved tubulin complex induced by the kine... -

+
Open data


ID or keywords:

Loading...

-
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 / Resolution of Sister Chromatid Cohesion / cellular response to interleukin-4 / regulation of cell migration / mitotic spindle organization / RHO GTPases Activate Formins / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / spindle pole / neuron migration / 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 / ciliary basal body / nuclear body / cilium / protein heterodimerization activity / cell division / GTPase activity / centrosome / ubiquitin protein ligase binding / GTP binding / nucleolus / ATP hydrolysis activity / nucleoplasm / ATP binding / metal ion binding / membrane / cytosol / cytoplasm
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 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more