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- PDB-7bjs: Crystal structure of Khc/atypical Tm1 complex -

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Basic information

Entry
Database: PDB / ID: 7bjs
TitleCrystal structure of Khc/atypical Tm1 complex
Components
  • Kinesin heavy chain
  • SD21996p
KeywordsTRANSPORT PROTEIN / triple coiled-coil / mRNA transport / protein-protein complex / Drosophila oocyte
Function / homology
Function and homology information


actin filament bundle organization / anterograde axonal transport of mitochondrion / anterograde dendritic transport / ovarian nurse cell to oocyte transport / mitochondrion distribution / larval locomotory behavior / oocyte microtubule cytoskeleton polarization / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization ...actin filament bundle organization / anterograde axonal transport of mitochondrion / anterograde dendritic transport / ovarian nurse cell to oocyte transport / mitochondrion distribution / larval locomotory behavior / oocyte microtubule cytoskeleton polarization / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification / pole plasm assembly / microtubule sliding / dorsal appendage formation / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / transport along microtubule / larval somatic muscle development / centrosome separation / anterograde dendritic transport of neurotransmitter receptor complex / actomyosin contractile ring / actin cap / microtubule plus-end / axo-dendritic transport / plus-end-directed microtubule motor activity / nuclear migration / stress granule disassembly / dendrite morphogenesis / microtubule motor activity / kinesin complex / synaptic vesicle transport / intracellular distribution of mitochondria / tropomyosin binding / microtubule-based movement / cytoskeletal motor activity / microtubule polymerization / mitotic cytokinesis / axon cytoplasm / dendrite cytoplasm / axonogenesis / muscle contraction / actin filament / actin filament organization / axon guidance / actin filament binding / mitotic cell cycle / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Tropomyosin / Tropomyosin / Kinesin-like protein / 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 heavy chain / SD21996p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDimitrova-Paternoga, L. / Jagtap, P.K.A. / Ephrussi, A. / Hennig, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP 1935 Germany
CitationJournal: Genes Dev. / Year: 2021
Title: Molecular basis of mRNA transport by a kinesin-1-atypical tropomyosin complex.
Authors: Dimitrova-Paternoga, L. / Jagtap, P.K.A. / Cyrklaff, A. / Lapouge, K. / Sehr, P. / Perez, K. / Heber, S. / Low, C. / Hennig, J. / Ephrussi, A.
History
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 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 heavy chain
B: Kinesin heavy chain
C: SD21996p


Theoretical massNumber of molelcules
Total (without water)30,9293
Polymers30,9293
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-64 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.770, 33.490, 126.000
Angle α, β, γ (deg.)90.000, 94.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 855 through 872 or (resid 873...
21(chain B and (resid 855 through 907 or (resid 908...

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
11SERSERVALVAL(chain A and (resid 855 through 872 or (resid 873...AA855 - 8723 - 20
12ARGARGARGARG(chain A and (resid 855 through 872 or (resid 873...AA87321
13SERSERARGARG(chain A and (resid 855 through 872 or (resid 873...AA855 - 9233 - 71
14SERSERARGARG(chain A and (resid 855 through 872 or (resid 873...AA855 - 9233 - 71
15SERSERARGARG(chain A and (resid 855 through 872 or (resid 873...AA855 - 9233 - 71
16SERSERARGARG(chain A and (resid 855 through 872 or (resid 873...AA855 - 9233 - 71
21SERSERLYSLYS(chain B and (resid 855 through 907 or (resid 908...BB855 - 9073 - 55
22GLUGLUGLUGLU(chain B and (resid 855 through 907 or (resid 908...BB90856
23SERSERARGARG(chain B and (resid 855 through 907 or (resid 908...BB855 - 9163 - 64
24SERSERARGARG(chain B and (resid 855 through 907 or (resid 908...BB855 - 9163 - 64
25SERSERARGARG(chain B and (resid 855 through 907 or (resid 908...BB855 - 9163 - 64
26SERSERARGARG(chain B and (resid 855 through 907 or (resid 908...BB855 - 9163 - 64
27SERSERARGARG(chain B and (resid 855 through 907 or (resid 908...BB855 - 9163 - 64

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Components

#1: Protein Kinesin heavy chain


Mass: 10588.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Khc, kin, CG7765 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17210
#2: Protein SD21996p / Tropomyosin 1 / isoform H


Mass: 9751.968 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FlyBase ID FBpp0088901 / Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Tm1, 10, 1305, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, chr3R:11122272..11122408, cTM, cTm, cTmII, Dm Tm1, Dm TmH33, Dm TmH34, Dmel\CG4898, DmTm1, l(3)02299, l(3)S130510, l(3)s2958, ...Gene: Tm1, 10, 1305, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, chr3R:11122272..11122408, cTM, cTm, cTmII, Dm Tm1, Dm TmH33, Dm TmH34, Dmel\CG4898, DmTm1, l(3)02299, l(3)S130510, l(3)s2958, mTmII, PmI, region 3, TM, Tm, TM1, tm1, TmH, TmH-33, TmH-34, TmH33, TmH34, TMII, TmII, tmII, Tmr33, Tmr34, TnH, TnH-33, TnH-34, tropomyosin, CG4898, Dmel_CG4898
Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q8IG84
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaAc, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.28→41.87 Å / Num. obs: 21116 / % possible obs: 98.5 % / Redundancy: 3.387 % / Biso Wilson estimate: 51.357 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.125 / Χ2: 1.113 / Net I/σ(I): 6.7 / Num. measured all: 71511
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.28-2.342.9691.0460.994186159514100.3451.26988.4
2.34-2.43.220.9771.165036156815640.5191.17799.7
2.4-2.473.5220.6991.735202147914770.6310.82799.9
2.47-2.553.5310.5852.15155146514600.7030.69199.7
2.55-2.633.4750.4992.514948142614240.8070.59199.9
2.63-2.723.420.452.824620135113510.8220.535100
2.72-2.833.290.3293.584359133613250.8990.39399.2
2.83-2.943.1850.2424.474026126912640.9490.29299.6
2.94-3.073.5460.2115.564223119811910.9580.2599.4
3.07-3.223.5480.1596.964180118411780.9760.18799.5
3.22-3.43.4690.1318.393809111110980.9860.15698.8
3.4-3.63.4590.10310.853677106910630.9870.12299.4
3.6-3.853.20.08112.5830149529420.990.09898.9
3.85-4.163.5760.06715.0933479419360.9920.07999.5
4.16-4.563.5560.0616.9228418087990.9950.07198.9
4.56-5.093.4680.06316.1926087607520.9950.07498.9
5.09-5.883.110.07712.6520686826650.9930.09397.5
5.88-7.23.5780.06414.0320975875860.9950.07699.8
7.2-10.193.360.04416.313714194080.9980.05297.4
10.19-41.873.3360.0419.247442452230.9980.04891

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly Ala triple helix

Resolution: 2.28→41.87 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.14 / Phase error: 32.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2781 1056 5 %
Rwork0.2281 20059 -
obs0.2307 21115 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.6 Å2 / Biso mean: 68.5137 Å2 / Biso min: 30.21 Å2
Refinement stepCycle: final / Resolution: 2.28→41.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 0 26 1596
Biso mean---62.37 -
Num. residues----198
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A376X-RAY DIFFRACTION6.639TORSIONAL
12B376X-RAY DIFFRACTION6.639TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.28-2.380.42981230.34782409253293
2.38-2.510.31611320.297824882620100
2.51-2.660.33231340.256425462680100
2.66-2.870.31831330.23342552268599
2.87-3.160.24861340.23162558269299
3.16-3.620.24511350.19762512264799
3.62-4.550.26511300.18262494262499
4.56-41.870.27211350.25092500263598
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)
1-0.06550.2037-0.03510.6106-0.20540.3940.1391-0.0221-0.07080.034-0.0312-0.04730.1486-0.09210.00190.3855-0.0073-0.0050.43610.01760.38817.694-0.13212.693
20.52840.111-0.0520.53040.44130.38730.04930.0196-0.03030.09550.07430.0343-0.13470.49710.00020.43930.03250.03010.37630.02020.449210.466-4.1476.179
30.07520.025-0.06620.1976-0.07470.07070.00350.0344-0.01290.0489-0.11250.41020.0938-0.35580.00060.6286-0.17090.04180.58310.01010.44286.794-1.78832.186
40.54950.1044-0.13320.41740.00840.05790.08850.1002-0.3029-0.0883-0.2428-0.05070.25390.1227-0.00020.34540.08940.00690.3943-0.01030.41082.538-8.19-14.027
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 855:923 )A855 - 923
2X-RAY DIFFRACTION2( CHAIN B AND RESID 855:916 )B855 - 916
3X-RAY DIFFRACTION3( CHAIN C AND RESID 258:277 )C258 - 277
4X-RAY DIFFRACTION4( CHAIN C AND RESID 278:324 )C278 - 324

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