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- PDB-3dc4: Crystal structure of the Drosophila kinesin family member NOD in ... -

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Basic information

Entry
Database: PDB / ID: 3dc4
TitleCrystal structure of the Drosophila kinesin family member NOD in complex with ADP
ComponentsKinesin-like protein Nod
KeywordsMOTOR PROTEIN / kinesin / catalytic domain / ATPase / microtubule / ADP / nucleotide-binding protein / ATP-binding / Coiled coil / Nucleotide-binding
Function / homology
Function and homology information


establishment of meiotic spindle orientation / distributive segregation / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / meiotic chromosome segregation / female meiotic nuclear division / microtubule plus-end binding / spindle assembly involved in female meiosis I / kinesin complex / microtubule motor activity ...establishment of meiotic spindle orientation / distributive segregation / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / meiotic chromosome segregation / female meiotic nuclear division / microtubule plus-end binding / spindle assembly involved in female meiosis I / kinesin complex / microtubule motor activity / microtubule-based movement / positive regulation of microtubule polymerization / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin-like protein / RuvA domain 2-like / 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 / Kinesin / Kinesin-like protein / RuvA domain 2-like / 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 Nod
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, molecular replacement / MAD / molecular replacement / Resolution: 1.9 Å
AuthorsCochran, J.C. / Mulko, N.K. / Kull, F.J.
CitationJournal: Cell / Year: 2009
Title: ATPase cycle of the nonmotile kinesin NOD allows microtubule end tracking and drives chromosome movement.
Authors: Jared C Cochran / Charles V Sindelar / Natasha K Mulko / Kimberly A Collins / Stephanie E Kong / R Scott Hawley / F Jon Kull /
Abstract: Segregation of nonexchange chromosomes during Drosophila melanogaster meiosis requires the proper function of NOD, a nonmotile kinesin-10. We have determined the X-ray crystal structure of the NOD ...Segregation of nonexchange chromosomes during Drosophila melanogaster meiosis requires the proper function of NOD, a nonmotile kinesin-10. We have determined the X-ray crystal structure of the NOD catalytic domain in the ADP- and AMPPNP-bound states. These structures reveal an alternate conformation of the microtubule binding region as well as a nucleotide-sensitive relay of hydrogen bonds at the active site. Additionally, a cryo-electron microscopy reconstruction of the nucleotide-free microtubule-NOD complex shows an atypical binding orientation. Thermodynamic studies show that NOD binds tightly to microtubules in the nucleotide-free state, yet other nucleotide states, including AMPPNP, are weakened. Our pre-steady-state kinetic analysis demonstrates that NOD interaction with microtubules occurs slowly with weak activation of ADP product release. Upon rapid substrate binding, NOD detaches from the microtubule prior to the rate-limiting step of ATP hydrolysis, which is also atypical for a kinesin. We propose a model for NOD's microtubule plus-end tracking that drives chromosome movement.
History
DepositionJun 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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.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.value / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein Nod
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7573
Polymers38,3061
Non-polymers4522
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.829, 75.715, 94.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kinesin-like protein Nod


Mass: 38305.562 Da / Num. of mol.: 1 / Fragment: Catalytic core domain (Residues 1-318)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: nod, NODA, CG1763 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)RIL / References: UniProt: P18105
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2444.98
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, hanging drop6.50.1 MES, 15% PEG 20000, Se-MET Derivative, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2772vapor diffusion, hanging drop6.50.1 MES, 15% PEG 20000, NATIVE PROTEIN, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A10.9790, 0.9796, 0.9184
SYNCHROTRONNSLS X6A20.9791
Detector
TypeIDDetectorDateDetails
ADSC1CCDApr 7, 2007TOROIDAL FOCUSING MIRROR
ADSC2CCDJul 12, 2007TOROIDAL FOCUSING MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111) CHANNEL CUTMADMx-ray1
2SI(111) CHANNEL CUTSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97961
30.91841
40.97911
ReflectionAv σ(I) over netI: 19.2 / Number: 220709 / Rmerge(I) obs: 0.099 / D res high: 2.3 Å / D res low: 20 Å / Num. obs: 28615 / % possible obs: 97.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2.32.4337097.110.421
2.42.5289397.310.411
2.52.6245797.410.334
2.62.7213497.810.303
2.7348199810.226
34747598.310.088
45270798.910.04
56117898.510.048
610128099.110.035
ReflectionResolution: 1.9→19 Å / Num. obs: 27088 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.81 % / Biso Wilson estimate: 30.315 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 8.2 / Net I/σ(I): 22.77
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.88 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4.9 / Num. measured obs: 18583 / Num. unique all: 18583 / Num. unique obs: 3809 / Rsym value: 35.4 / % possible all: 98.8

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Phasing

Phasing
Method
MAD
molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.575 / Packing: 0.453
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation2.5 Å15 Åfast direct98.5 0
Translation2.3 Å15 Ågeneral98.6 0

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
SOLVE2.13phasing
RESOLVE2.13phasing
PDB_EXTRACT3.005data extraction
CNSphasing
RefinementMethod to determine structure: MAD, molecular replacement / Resolution: 1.9→19 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1629446.125 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1320 4.9 %RANDOM
Rwork0.227 ---
obs-27088 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.77 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å20 Å2
2---7 Å20 Å2
3---4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 28 312 2587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d2.27
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 202 4.8 %
Rwork0.256 3975 -
all-4177 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5adp_cns_jcc.paradp_cns_jcc.top

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