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- PDB-8whl: Crystal structure of CLASP2 in complex with CENP-E -

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Basic information

Entry
Database: PDB / ID: 8whl
TitleCrystal structure of CLASP2 in complex with CENP-E
Components
  • CLIP-associating protein 2
  • Centromere-associated protein E
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


lateral attachment of mitotic spindle microtubules to kinetochore / presynaptic cytoskeleton organization / cortical microtubule plus-end / microtubule plus-end directed mitotic chromosome migration / negative regulation of wound healing, spreading of epidermal cells / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / vesicle targeting / regulation of gastrulation / mitotic chromosome movement towards spindle pole / microtubule anchoring ...lateral attachment of mitotic spindle microtubules to kinetochore / presynaptic cytoskeleton organization / cortical microtubule plus-end / microtubule plus-end directed mitotic chromosome migration / negative regulation of wound healing, spreading of epidermal cells / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / vesicle targeting / regulation of gastrulation / mitotic chromosome movement towards spindle pole / microtubule anchoring / metaphase chromosome alignment / positive regulation of extracellular matrix disassembly / basal cortex / mitotic spindle midzone / microtubule organizing center organization / kinetochore binding / Role of ABL in ROBO-SLIT signaling / kinetochore microtubule / establishment of mitotic spindle localization / negative regulation of focal adhesion assembly / dystroglycan binding / regulation of epithelial to mesenchymal transition / negative regulation of microtubule depolymerization / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / microtubule nucleation / regulation of microtubule-based process / microtubule plus-end binding / Kinesins / regulation of mitotic metaphase/anaphase transition / microtubule motor activity / negative regulation of stress fiber assembly / exit from mitosis / regulation of axon extension / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic metaphase chromosome alignment / establishment or maintenance of cell polarity / Golgi organization / platelet-derived growth factor receptor-beta signaling pathway / cell leading edge / regulation of microtubule polymerization / microtubule organizing center / positive regulation of exocytosis / chromosome, centromeric region / positive regulation of epithelial cell migration / mitotic spindle assembly / positive regulation of protein kinase activity / regulation of microtubule polymerization or depolymerization / spindle midzone / axonal growth cone / intercellular bridge / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / protein tyrosine kinase binding / mitotic spindle organization / protein localization to plasma membrane / spindle microtubule / chromosome segregation / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / trans-Golgi network / kinetochore / microtubule cytoskeleton organization / ruffle membrane / actin filament binding / mitotic spindle / Separation of Sister Chromatids / mitotic cell cycle / chromosome / microtubule cytoskeleton / midbody / cell cortex / microtubule binding / microtubule / cell division / intracellular membrane-bounded organelle / centrosome / glutamatergic synapse / Golgi apparatus / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CLASP N-terminal domain / CLASP N terminal / Centrosomal protein CEP104-like, TOG domain / TOG domain / TOG / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. ...CLASP N-terminal domain / CLASP N terminal / Centrosomal protein CEP104-like, TOG domain / TOG domain / TOG / 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 / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / MALONIC ACID / CLIP-associating protein 2 / Centromere-associated protein E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJia, X. / Wei, Z.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971131 China
National Natural Science Foundation of China (NSFC)32170697 China
National Natural Science Foundation of China (NSFC)32370743 China
National Natural Science Foundation of China (NSFC)32371009 China
CitationJournal: Nat Commun / Year: 2024
Title: CLASP-mediated competitive binding in protein condensates directs microtubule growth.
Authors: Jia, X. / Lin, L. / Guo, S. / Zhou, L. / Jin, G. / Dong, J. / Xiao, J. / Xie, X. / Li, Y. / He, S. / Wei, Z. / Yu, C.
History
DepositionSep 23, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: CLIP-associating protein 2
D: CLIP-associating protein 2
F: Centromere-associated protein E
H: Centromere-associated protein E
C: CLIP-associating protein 2
G: Centromere-associated protein E
A: CLIP-associating protein 2
E: Centromere-associated protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,07211
Polymers136,8498
Non-polymers2223
Water00
1
B: CLIP-associating protein 2
F: Centromere-associated protein E
A: CLIP-associating protein 2
E: Centromere-associated protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6477
Polymers68,4254
Non-polymers2223
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: CLIP-associating protein 2
H: Centromere-associated protein E
C: CLIP-associating protein 2
G: Centromere-associated protein E


Theoretical massNumber of molelcules
Total (without water)68,4254
Polymers68,4254
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.221, 106.221, 327.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
CLIP-associating protein 2 / Cytoplasmic linker-associated protein 2 / Protein Orbit homolog 2 / hOrbit2


Mass: 26443.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLASP2, KIAA0627 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75122
#2: Protein
Centromere-associated protein E / Centromere protein E / CENP-E / Kinesin-7 / Kinesin-related protein CENPE


Mass: 7768.564 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02224
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
Has ligand of interestN

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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: 3.89 Å3/Da / Density % sol: 68.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 6.5 and 1.4 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 34412 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.051 / Rrim(I) all: 0.128 / Χ2: 0.888 / Net I/σ(I): 5.2 / Num. measured all: 217234
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.2-3.266.31.03517050.5450.840.4491.130.70499.9
3.26-3.315.80.84217350.6070.8690.3750.9250.7399.8
3.31-3.3860.71616730.6730.8970.3150.7840.7399.9
3.38-3.456.60.60917490.8160.9480.2560.6610.752100
3.45-3.526.60.48717160.8380.9550.2050.5290.791100
3.52-3.66.50.37217010.9050.9750.1580.4050.822100
3.6-3.696.50.28917320.9350.9830.1230.3150.841100
3.69-3.796.40.23617460.9530.9880.1010.2570.89100
3.79-3.916.30.21216930.960.990.0920.2320.941100
3.91-4.036.10.1817050.9690.9920.0790.1970.939100
4.03-4.185.70.15517160.9740.9930.070.171.013100
4.18-4.346.70.13517120.9770.9940.0570.1461.022100
4.34-4.546.60.1217370.9810.9950.0510.131.07799.9
4.54-4.786.50.10917170.9880.9970.0470.1181.014100
4.78-5.086.40.10417300.9810.9950.0450.1140.99299.9
5.08-5.475.90.117050.9840.9960.0450.110.93699.7
5.47-6.026.60.10417280.9860.9960.0440.1130.947100
6.02-6.896.50.09517230.990.9970.040.1030.93199.9
6.89-8.6760.07517270.9920.9980.0330.0820.84199.8
8.67-506.10.0717620.9930.9980.0310.0770.81599.5

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→46.89 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 1707 4.99 %
Rwork0.2463 --
obs0.2479 34200 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8740 0 15 0 8755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028863
X-RAY DIFFRACTIONf_angle_d0.48411971
X-RAY DIFFRACTIONf_dihedral_angle_d19.2383386
X-RAY DIFFRACTIONf_chiral_restr0.0361449
X-RAY DIFFRACTIONf_plane_restr0.0041516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.290.33321390.31522708X-RAY DIFFRACTION100
3.29-3.40.35681400.292718X-RAY DIFFRACTION100
3.4-3.520.32311430.28782701X-RAY DIFFRACTION100
3.52-3.660.33481450.28052709X-RAY DIFFRACTION100
3.66-3.830.32741450.25672710X-RAY DIFFRACTION100
3.83-4.030.29691430.26452684X-RAY DIFFRACTION100
4.03-4.280.27871410.24632723X-RAY DIFFRACTION100
4.28-4.610.28661450.23382723X-RAY DIFFRACTION100
4.61-5.080.25831410.24232708X-RAY DIFFRACTION100
5.08-5.810.2781450.26762697X-RAY DIFFRACTION100
5.81-7.310.30581420.27982714X-RAY DIFFRACTION100
7.32-46.890.21791380.19692698X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.91460.1504-2.03821.4331-1.75325.9411-0.9982-0.81521.58332.390.4579-0.125-1.15690.40250.4331.32160.4142-0.41060.5947-0.58351.7447-14.9936-15.62740.3418
26.7691-1.78682.01892.3086-1.87322.48430.252-0.70450.06170.3456-0.6489-0.4288-0.73670.75770.84551.012-0.0879-0.07741.1003-0.27611.4199-15.5713-14.518-9.3166
36.91244.35861.46875.5721-4.16949.5574-0.9342-2.74962.00650.72911.08711.1508-0.8454-1.77760.46980.84120.0433-0.05120.9829-0.4040.5564-14.3279-25.7307-4.9095
49.1254-1.1972-0.07118.2836-0.01766.77430.0807-0.04791.1093-0.25530.02070.5163-1.4248-0.2162-0.00840.78190.05060.01870.515-0.11940.563-15.0458-26.7254-18.0147
51.77930.1033-1.83813.03150.75624.56420.2651-0.0373-0.1688-0.0016-0.3265-0.05660.6793-0.14780.14430.5790.119-0.12710.6582-0.0390.4336-10.8339-44.8205-28.4416
66.03360.25620.41913.73832.36194.00420.02380.5998-0.74040.1093-1.4698-0.6789-1.2207-0.87270.70361.10810.07850.05291.03240.08470.5688-6.6799-47.1024-42.7116
75.0364-0.4304-3.15097.45472.40717.1016-0.65480.4339-1.6142-0.29150.20241.04151.7476-0.27070.21720.9684-0.1334-0.06050.6842-0.08681.179-24.0771-62.1311-20.5229
86.1738-1.6088-2.09452.69182.32065.51450.1584-1.2806-0.28570.6093-0.3880.2429-0.46690.01530.0420.8537-0.20030.06190.94330.01450.6237-33.8159-39.5569-5.9783
92.89520.85490.84213.44711.11250.3112-0.460.46920.97440.9490.56950.3867-0.11410.69650.06771.4442-0.0148-0.15480.880.20050.7811-5.67-16.1496-37.6055
100.2011-0.39150.56881.3287-1.06411.048-0.3516-0.1451-0.5075-1.0590.8020.46960.8528-0.3619-0.04971.7388-0.09810.38651.0062-0.22651.5411-52.4526-56.1199-13.9566
117.4795-7.9652-1.0729.65712.90962.8103-1.36582.42530.0346-2.35112.9038-3.04220.272-2.7031-0.66391.0896-0.7395-0.11591.62930.471.4493-90.4832-71.5192-8.8291
123.2814-2.54621.23083.9344-3.77174.5133-0.7818-2.8902-0.5979-1.87920.04170.256-0.38890.76710.35691.933-0.03210.54221.31940.19082.3259-83.8695-64.6340.3972
137.03620.4667-4.16990.2761-0.2043.4409-0.1753-0.4249-1.7969-2.1155-0.1818-1.25180.88321.0974-0.21681.2511-0.12830.29680.4866-0.06342.155-81.6183-69.7547-13.3757
147.1980.4127-1.77086.6703-0.99844.42750.39310.8464-1.5704-0.14710.2356-0.86151.50580.438-0.02140.91590.24080.06860.645-0.12991.0253-84.1696-60.6193-13.7011
155.57911.33120.95775.9028-1.7374.10470.67670.0781-1.0752-0.6571-0.0061-0.91771.3860.1823-0.01790.7429-0.02240.05560.8324-0.18150.7923-80.0293-51.9967-16.71
165.74830.3082-0.12616.9647-1.5132.9834-0.01581.26650.2693-0.6557-0.0582-0.39070.18590.4738-0.02120.70450.04770.1090.9245-0.01750.6164-77.8626-37.3524-27.5721
173.2639-1.8266-1.18351.6267-1.04545.29810.10421.10280.3256-2.0221-0.9052-2.0270.86741.93720.55831.35060.17940.62211.5780.29491.2377-64.7486-31.4608-33.6805
181.4302-1.1741-0.14711.39681.32552.8399-0.79790.1725-0.46480.60861.48850.29330.8887-0.748-0.60211.161-0.15810.37450.9676-0.0841.2374-59.3591-56.4375-18.6246
199.66543.9830.81086.2208-3.39487.90990.20140.53960.2346-0.81860.1146-0.4738-0.17190.7395-0.03470.8928-0.03730.34480.82250.03350.7778-9.1783-19.62-80.3225
206.86511.0568-3.64972.7245-0.28935.2623-0.02320.08730.6671-0.05520.1396-0.2625-0.08790.0616-0.13920.59030.1454-0.11870.5643-0.01220.4715-25.1877-27.2109-65.0002
219.57230.7557-2.70346.4082-0.20883.0707-0.151-0.55040.27080.84470.52860.58370.6652-0.6642-0.3360.80640.1111-0.0790.86120.1070.4131-39.2166-27.7601-48.922
221.94661.69250.86815.08992.44082.2431-1.28670.21340.4233-2.24550.7347-0.461-0.6890.09380.38051.09360.0992-0.15760.91530.00830.7426-10.5001-12.1033-39.4517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1253 through 1265 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1266 through 1290 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1291 through 1310 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1311 through 1371 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1372 through 1457 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1458 through 1478 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1253 through 1351 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1352 through 1478 )
9X-RAY DIFFRACTION9chain 'F' and (resid 494 through 548 )
10X-RAY DIFFRACTION10chain 'H' and (resid 494 through 548 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1255 through 1265 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1266 through 1271 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1272 through 1293 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1294 through 1331 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1332 through 1371 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1372 through 1459 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1460 through 1477 )
18X-RAY DIFFRACTION18chain 'G' and (resid 496 through 547 )
19X-RAY DIFFRACTION19chain 'A' and (resid 1251 through 1310 )
20X-RAY DIFFRACTION20chain 'A' and (resid 1311 through 1431 )
21X-RAY DIFFRACTION21chain 'A' and (resid 1432 through 1478 )
22X-RAY DIFFRACTION22chain 'E' and (resid 496 through 547 )

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