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- PDB-5ow5: p60p80-CAMSAP complex -

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Basic information

Entry
Database: PDB / ID: 5ow5
Titlep60p80-CAMSAP complex
Components
  • Calmodulin-regulated spectrin-associated protein
  • Katanin p60 ATPase-containing subunit A1
  • Katanin p80 WD40 repeat-containing subunit B1
KeywordsHYDROLASE / Katanin / CAMSAP / severing enzyme / MICROTUBULE / cytoskeleton
Function / homology
Function and homology information


ATPase regulator activity / regulation of organelle organization / zonula adherens maintenance / katanin complex / microtubule minus-end / protein transport along microtubule / regulation of Golgi organization / microtubule anchoring / microtubule-severing ATPase / microtubule severing ATPase activity ...ATPase regulator activity / regulation of organelle organization / zonula adherens maintenance / katanin complex / microtubule minus-end / protein transport along microtubule / regulation of Golgi organization / microtubule anchoring / microtubule-severing ATPase / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole / microtubule severing / establishment or maintenance of microtubule cytoskeleton polarity / positive regulation of microtubule depolymerization / cilium movement / microtubule minus-end binding / epithelial cell-cell adhesion / zonula adherens / negative regulation of microtubule depolymerization / establishment of epithelial cell apical/basal polarity / motile cilium / embryo development ending in birth or egg hatching / microtubule depolymerization / regulation of focal adhesion assembly / spectrin binding / dynein complex binding / regulation of microtubule polymerization / mitotic spindle pole / axoneme / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / regulation of cell migration / isomerase activity / ciliary basal body / microtubule cytoskeleton organization / positive regulation of neuron projection development / spindle pole / spindle / neuron projection development / microtubule cytoskeleton / actin filament binding / midbody / growth cone / microtubule binding / microtubule / in utero embryonic development / calmodulin binding / positive regulation of apoptotic process / cell cycle / protein heterodimerization activity / axon / cell division / centrosome / neuronal cell body / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Katanin p80 WD40 repeat-containing subunit B1 / Katanin p80 subunit, C-terminal / con80 domain of Katanin / CAMSAP, spectrin and Ca2+/calmodulin-binding region / Spectrin-binding region of Ca2+-Calmodulin / CKK domain / Calmodulin-regulated spectrin-associated protein / CKK domain superfamily / Microtubule-binding calmodulin-regulated spectrin-associated / CKK domain profile. ...Katanin p80 WD40 repeat-containing subunit B1 / Katanin p80 subunit, C-terminal / con80 domain of Katanin / CAMSAP, spectrin and Ca2+/calmodulin-binding region / Spectrin-binding region of Ca2+-Calmodulin / CKK domain / Calmodulin-regulated spectrin-associated protein / CKK domain superfamily / Microtubule-binding calmodulin-regulated spectrin-associated / CKK domain profile. / Microtubule-binding calmodulin-regulated spectrin-associated / Katanin p60 subunit A1 / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT domain superfamily / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain / PRC-barrel-like superfamily / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Katanin p60 ATPase-containing subunit A1 / Calmodulin-regulated spectrin-associated protein 3 / Katanin p80 WD40 repeat-containing subunit B1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRezabkova, L. / Capitani, G. / Prota, A.E. / Kammerer, R.A. / Steinmetz, M.O.
CitationJournal: Structure / Year: 2018
Title: Structural Basis of Formation of the Microtubule Minus-End-Regulating CAMSAP-Katanin Complex.
Authors: Jiang, K. / Faltova, L. / Hua, S. / Capitani, G. / Prota, A.E. / Landgraf, C. / Volkmer, R. / Kammerer, R.A. / Steinmetz, M.O. / Akhmanova, A.
History
DepositionAug 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Katanin p80 WD40 repeat-containing subunit B1
B: Katanin p60 ATPase-containing subunit A1
C: Katanin p80 WD40 repeat-containing subunit B1
D: Katanin p60 ATPase-containing subunit A1
E: Calmodulin-regulated spectrin-associated protein
F: Calmodulin-regulated spectrin-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2478
Polymers68,0796
Non-polymers1682
Water5,567309
1
A: Katanin p80 WD40 repeat-containing subunit B1
B: Katanin p60 ATPase-containing subunit A1
E: Calmodulin-regulated spectrin-associated protein


Theoretical massNumber of molelcules
Total (without water)34,0393
Polymers34,0393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-33 kcal/mol
Surface area13330 Å2
MethodPISA
2
C: Katanin p80 WD40 repeat-containing subunit B1
D: Katanin p60 ATPase-containing subunit A1
F: Calmodulin-regulated spectrin-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2085
Polymers34,0393
Non-polymers1682
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-26 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.330, 79.060, 99.060
Angle α, β, γ (deg.)90.00, 94.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Katanin p80 WD40 repeat-containing subunit B1 / Katanin p80 subunit B1 / p80 katanin


Mass: 23351.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Katnb1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BG40
#2: Protein Katanin p60 ATPase-containing subunit A1 / Katanin p60 subunit A1 / p60 katanin


Mass: 9534.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Katna1, KATNA1 / Production host: Escherichia coli (E. coli) / References: UniProt: E9PZI6, EC: 3.6.4.3

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Calmodulin-regulated spectrin-associated protein


Mass: 1153.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q80VC9*PLUS

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Non-polymers , 3 types, 311 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 20% PEG 3350, 0.1 M BisTris propane (pH 5.5), 0.2 M NaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→41.9 Å / Num. obs: 59910 / % possible obs: 97.5 % / Redundancy: 11.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.022 / Net I/σ(I): 17.8
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.038 / Num. unique obs: 8846 / CC1/2: 0.656 / Rpim(I) all: 0.445 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2875: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LB7

5lb7


Resolution: 1.7→41.86 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 1018 1.7 %
Rwork0.1908 --
obs0.1914 59903 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 11 309 4345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094137
X-RAY DIFFRACTIONf_angle_d0.8975578
X-RAY DIFFRACTIONf_dihedral_angle_d10.4732547
X-RAY DIFFRACTIONf_chiral_restr0.05667
X-RAY DIFFRACTIONf_plane_restr0.006687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.78970.3531350.3087828X-RAY DIFFRACTION91
1.7897-1.90180.31061460.26528398X-RAY DIFFRACTION97
1.9018-2.04860.24931440.22858373X-RAY DIFFRACTION98
2.0486-2.25480.24841470.19168478X-RAY DIFFRACTION98
2.2548-2.5810.21171470.18898517X-RAY DIFFRACTION99
2.581-3.25160.26121490.19198569X-RAY DIFFRACTION99
3.2516-41.87250.19581500.16668722X-RAY DIFFRACTION100
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)
18.2856-6.4848-3.4097.32683.61964.2967-0.2202-0.2051-0.09660.25440.1583-0.48080.22310.45460.02110.1117-0.00830.00460.21810.05730.2957122.9859145.6866-53.4593
21.26840.5231-0.14062.2899-0.33671.78910.04860.06370.0248-0.0408-0.05630.1316-0.2354-0.05770.03230.1150.0237-0.02160.18260.00910.1808112.664179.2687-61.6058
32.3356-2.3969-0.3516.8281-0.83011.79260.18360.1716-0.1153-0.661-0.2453-0.00680.28640.08220.05920.20380.0227-0.00740.1988-0.00460.1304118.2983144.7329-62.3804
41.8370.18540.94311.8324-0.40974.18940.06420.14260.2122-0.0497-0.2621-0.1431-0.73370.83450.11940.81-0.0832-0.03670.50370.070.2024126.0843186.2471-93.5766
50.86870.38630.3791.99950.01231.78240.0069-0.13460.0451-0.2269-0.1320.14750.4979-0.1380.0860.78670.0376-0.02460.3711-0.02510.1921114.0992153.8213-87.3757
60.5723-0.5075-0.10672.155-1.02991.78340.07580.14960.1441-0.0579-0.22730.0433-0.90550.15610.02390.77980.0052-0.04560.39690.0130.1653120.7334187.1609-85.4552
74.4288-4.33783.61515.0466-2.68863.862-0.04660.06190.4415-0.4506-0.0437-1.7747-0.21281.3325-0.10340.2081-0.01780.01730.41110.02810.5099127.3871156.8799-53.1387
88.39193.5231-4.61042.3779-4.16058.0590.1054-0.4253-0.08150.0708-0.1377-0.49930.00620.67740.05060.63590.08870.03030.481-0.04230.3087130.6637175.6329-92.7224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 485 through 508)
2X-RAY DIFFRACTION2chain 'A' and (resid 509 through 657)
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 78)
4X-RAY DIFFRACTION4chain 'C' and (resid 486 through 508)
5X-RAY DIFFRACTION5chain 'C' and (resid 509 through 657)
6X-RAY DIFFRACTION6chain 'D' and (resid 2 through 77)
7X-RAY DIFFRACTION7chain 'E' and (resid 8 through 17)
8X-RAY DIFFRACTION8chain 'F' and (resid 8 through 17)

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