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- PDB-1cz7: THE CRYSTAL STRUCTURE OF A MINUS-END DIRECTED MICROTUBULE MOTOR P... -

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Basic information

Entry
Database: PDB / ID: 1cz7
TitleTHE CRYSTAL STRUCTURE OF A MINUS-END DIRECTED MICROTUBULE MOTOR PROTEIN NCD REVEALS VARIABLE DIMER CONFORMATIONS
ComponentsMICROTUBULE MOTOR PROTEIN NCDMotor protein
KeywordsCONTRACTILE PROTEIN / NCD CRYSTAL STRUCTURE / MICROTUBULE MOTORS / KINESIN SUPERFAMILY
Function / homology
Function and homology information


minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / spindle assembly involved in female meiosis / minus-end-directed microtubule motor activity / regulation of mitotic spindle assembly ...minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / spindle assembly involved in female meiosis / minus-end-directed microtubule motor activity / regulation of mitotic spindle assembly / microtubule bundle formation / meiotic spindle / mitotic centrosome separation / spindle organization / mitotic spindle assembly / mRNA transport / mitotic spindle organization / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / spindle / microtubule binding / hydrolase activity / cell division / centrosome / protein homodimerization activity / ATP binding / nucleus / cytosol
Similarity search - Function
Kinesin motor domain / Kinesin / 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 ...Kinesin motor domain / Kinesin / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein claret segregational
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsKozielski, F.K. / De Bonis, S. / Burmeister, W. / Cohen-Addad, C. / Wade, R.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The crystal structure of the minus-end-directed microtubule motor protein ncd reveals variable dimer conformations.
Authors: Kozielski, F. / De Bonis, S. / Burmeister, W.P. / Cohen-Addad, C. / Wade, R.H.
History
DepositionSep 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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.ptnr1_label_seq_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_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_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_conn.ptnr2_label_seq_id / _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: MICROTUBULE MOTOR PROTEIN NCD
B: MICROTUBULE MOTOR PROTEIN NCD
C: MICROTUBULE MOTOR PROTEIN NCD
D: MICROTUBULE MOTOR PROTEIN NCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,27412
Polymers184,4684
Non-polymers1,8068
Water2,666148
1
A: MICROTUBULE MOTOR PROTEIN NCD
B: MICROTUBULE MOTOR PROTEIN NCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1376
Polymers92,2342
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-52 kcal/mol
Surface area32230 Å2
MethodPISA
2
C: MICROTUBULE MOTOR PROTEIN NCD
D: MICROTUBULE MOTOR PROTEIN NCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1376
Polymers92,2342
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-62 kcal/mol
Surface area35480 Å2
MethodPISA
3
C: MICROTUBULE MOTOR PROTEIN NCD
D: MICROTUBULE MOTOR PROTEIN NCD
hetero molecules

C: MICROTUBULE MOTOR PROTEIN NCD
D: MICROTUBULE MOTOR PROTEIN NCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,27412
Polymers184,4684
Non-polymers1,8068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area10740 Å2
ΔGint-125 kcal/mol
Surface area69520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.194, 148.827, 261.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein
MICROTUBULE MOTOR PROTEIN NCD / Motor protein / NCD / CLARET SEGREGATIONAL PROTEIN


Mass: 46117.004 Da / Num. of mol.: 4 / Fragment: CONSTRUCT MC5 FROM NCD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P20480
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / 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.: 148 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, NACL, MGCL2, K3PO4, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal
*PLUS
Density % sol: 58.6 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
26.8 %PEG80001drop
31 M1dropNaCl
42 mMATP1drop
53.5 mMdithiothreitol1drop
610 mM1dropMgCl2
725 mMsodium phosphate1drop
825 mMsodium phophate1reservoir
913.5 %PEG80001reservoir
102 M1reservoirNaCl
117 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 50539 / Num. obs: 48773 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.085
Reflection shellHighest resolution: 2.9 Å
Reflection
*PLUS
Num. measured all: 136320
Reflection shell
*PLUS
Lowest resolution: 3 Å / Rmerge(I) obs: 0.28

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: SIMULATED ANNEALING, NCS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2463 5 %RANDOM
Rwork0.258 ---
obs0.258 48773 96.5 %-
all-50539 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.632 Å20 Å20 Å2
2--15.315 Å20 Å2
3----29.946 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11179 0 112 148 11439
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 40 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6

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