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- PDB-3nry: Insights into anti-parallel microtubule crosslinking by PRC1, a c... -

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Basic information

Entry
Database: PDB / ID: 3nry
TitleInsights into anti-parallel microtubule crosslinking by PRC1, a conserved microtubule binding protein
ComponentsProtein regulator of cytokinesis 1
KeywordsPROTEIN BINDING / spectrin fold / microtubule binding protein
Function / homology
Function and homology information


contractile ring / mitotic spindle midzone assembly / mitotic spindle elongation / mitotic spindle midzone / RHO GTPases activate CIT / intercellular bridge / kinesin binding / regulation of cytokinesis / spindle microtubule / spindle ...contractile ring / mitotic spindle midzone assembly / mitotic spindle elongation / mitotic spindle midzone / RHO GTPases activate CIT / intercellular bridge / kinesin binding / regulation of cytokinesis / spindle microtubule / spindle / microtubule cytoskeleton organization / spindle pole / microtubule cytoskeleton / chromosome / midbody / microtubule binding / cell division / positive regulation of cell population proliferation / protein kinase binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1520 / Microtubule-associated protein, MAP65/Ase1/PRC1 / Microtubule associated protein (MAP65/ASE1 family) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein regulator of cytokinesis 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKapoor, T.M. / Subramanian, R. / Wilson-Kubalek, E.M. / Arthur, C.P. / Bick, M.J. / Campbell, E.A. / Darst, S.A. / Milligan, R.A.
CitationJournal: Cell / Year: 2010
Title: Insights into antiparallel microtubule crosslinking by PRC1, a conserved nonmotor microtubule binding protein.
Authors: Radhika Subramanian / Elizabeth M Wilson-Kubalek / Christopher P Arthur / Matthew J Bick / Elizabeth A Campbell / Seth A Darst / Ronald A Milligan / Tarun M Kapoor /
Abstract: Formation of microtubule architectures, required for cell shape maintenance in yeast, directional cell expansion in plants and cytokinesis in eukaryotes, depends on antiparallel microtubule ...Formation of microtubule architectures, required for cell shape maintenance in yeast, directional cell expansion in plants and cytokinesis in eukaryotes, depends on antiparallel microtubule crosslinking by the conserved MAP65 protein family. Here, we combine structural and single molecule fluorescence methods to examine how PRC1, the human MAP65, crosslinks antiparallel microtubules. We find that PRC1's microtubule binding is mediated by a structured domain with a spectrin-fold and an unstructured Lys/Arg-rich domain. These two domains, at each end of a homodimer, are connected by a linkage that is flexible on single microtubules, but forms well-defined crossbridges between antiparallel filaments. Further, we show that PRC1 crosslinks are compliant and do not substantially resist filament sliding by motor proteins in vitro. Together, our data show how MAP65s, by combining structural flexibility and rigidity, tune microtubule associations to establish crosslinks that selectively "mark" antiparallel overlap in dynamic cytoskeletal networks.
History
DepositionJul 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein regulator of cytokinesis 1


Theoretical massNumber of molelcules
Total (without water)16,0731
Polymers16,0731
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.043, 51.043, 90.347
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Protein regulator of cytokinesis 1


Mass: 16072.549 Da / Num. of mol.: 1 / Fragment: UNP residues 341-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRC1 / Production host: Escherichia coli (E. coli) / References: UniProt: O43663
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1:1 v/v protein (50 mg/ml in 80 mM PIPES, pH 6.8, 1 mM MgCl2, 1 mM EDTA, 150 mM KCl) and reservoir buffer (100 mM CHES pH 9.5, 30 % PEG 3000), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2009 / Details: Single crystal side bounce
RadiationMonochromator: single crystal side bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 17696 / Num. obs: 17342 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 20.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2 / Num. unique all: 914 / Rsym value: 0.469 / % possible all: 97.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.103 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R Free: 0.199
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27378 435 4.8 %RANDOM
Rwork0.23788 ---
all0.239 17696 --
obs0.23953 8670 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.778 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20.71 Å20 Å2
2--1.42 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 0 72 1114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221063
X-RAY DIFFRACTIONr_bond_other_d0.0010.02757
X-RAY DIFFRACTIONr_angle_refined_deg1.0471.9381422
X-RAY DIFFRACTIONr_angle_other_deg0.79131834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9665123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33824.65558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98215208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.597157
X-RAY DIFFRACTIONr_chiral_restr0.0640.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.661.5621
X-RAY DIFFRACTIONr_mcbond_other0.1141.5250
X-RAY DIFFRACTIONr_mcangle_it1.2982981
X-RAY DIFFRACTIONr_scbond_it1.9663442
X-RAY DIFFRACTIONr_scangle_it3.3194.5441
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.995→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 29 -
Rwork0.275 650 -
obs--98.69 %

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