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- PDB-5itz: Crystal structure of the SAC domain of CPAP in a complex with Tub... -

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Basic information

Entry
Database: PDB / ID: 5itz
TitleCrystal structure of the SAC domain of CPAP in a complex with Tubulin and Darpin
Components
  • Centromere protein J
  • Designed ankyrin repeat protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsSTRUCTURAL PROTEIN / Tubulin / CPAP / Centriole
Function / homology
Function and homology information


astral microtubule nucleation / centriole elongation / gamma-tubulin small complex / positive regulation of centriole elongation / positive regulation of establishment of protein localization / regulation of centriole replication / procentriole replication complex / positive regulation of non-motile cilium assembly / positive regulation of centriole replication / motile cilium assembly ...astral microtubule nucleation / centriole elongation / gamma-tubulin small complex / positive regulation of centriole elongation / positive regulation of establishment of protein localization / regulation of centriole replication / procentriole replication complex / positive regulation of non-motile cilium assembly / positive regulation of centriole replication / motile cilium assembly / positive regulation of spindle assembly / microtubule nucleation / non-motile cilium assembly / gamma-tubulin binding / positive regulation of axon guidance / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / smoothened signaling pathway / microtubule polymerization / centriole replication / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / cytoplasmic microtubule / microtubule-based process / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / cellular response to interleukin-4 / centriole / tubulin binding / AURKA Activation by TPX2 / ciliary basal body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of receptor signaling pathway via JAK-STAT / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-stranded RNA binding / mitotic cell cycle / nervous system development / microtubule / transcription coactivator activity / protein heterodimerization activity / cell division / protein domain specific binding / GTPase activity / centrosome / ubiquitin protein ligase binding / GTP binding / protein kinase binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
T-complex protein 10, C-terminal domain / T-complex protein 10 family / T-complex protein 10 C-terminus / : / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. ...T-complex protein 10, C-terminal domain / T-complex protein 10 family / T-complex protein 10 C-terminus / : / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-LOC / Tubulin alpha-1B chain / Tubulin beta-2B chain / Centromere protein J
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSharma, A. / Steinmetz, M.O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_138659 Switzerland
CitationJournal: Dev.Cell / Year: 2016
Title: Centriolar CPAP/SAS-4 Imparts Slow Processive Microtubule Growth.
Authors: Sharma, A. / Aher, A. / Dynes, N.J. / Frey, D. / Katrukha, E.A. / Jaussi, R. / Grigoriev, I. / Croisier, M. / Kammerer, R.A. / Akhmanova, A. / Gonczy, P. / Steinmetz, M.O.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_entity_src_syn
Revision 1.2Jul 29, 2020Group: Derived calculations / Structure summary / Category: entity / pdbx_struct_conn_angle / struct_conn
Item: _entity.src_method / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._entity.src_method / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Jan 10, 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: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
D: Centromere protein J
F: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8408
Polymers128,4494
Non-polymers1,3904
Water8,521473
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-48 kcal/mol
Surface area35660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.080, 85.340, 98.690
Angle α, β, γ (deg.)90.00, 91.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ABDF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856
#3: Protein Centromere protein J / / CENP-J / Centrosomal P4.1-associated protein / LAG-3-associated protein / LYST-interacting protein 1


Mass: 14889.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPJ, CPAP, LAP, LIP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HC77
#4: Protein Designed ankyrin repeat protein (DARPIN) D1


Mass: 13355.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 477 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-LOC / N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide / COLCHICINE / Colchicine


Mass: 399.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO6 / Comment: medication, antiinflammatory*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 1.91 Å3/Da / Density % sol: 35.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 550 mono methyl ether (MME) and 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→64.5 Å / Num. obs: 51519 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.07782 / Net I/σ(I): 18.11
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.7067

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DRX

4drx


Resolution: 2.2→52.644 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.4
RfactorNum. reflection% reflection
Rfree0.2174 2001 3.89 %
Rwork0.1773 --
obs0.1789 51503 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→52.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7702 0 90 473 8265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087977
X-RAY DIFFRACTIONf_angle_d1.0210838
X-RAY DIFFRACTIONf_dihedral_angle_d19.6592875
X-RAY DIFFRACTIONf_chiral_restr0.0591205
X-RAY DIFFRACTIONf_plane_restr0.0051403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.32741390.27573520X-RAY DIFFRACTION100
2.255-2.31590.31531470.25063487X-RAY DIFFRACTION100
2.3159-2.38410.27481490.24073554X-RAY DIFFRACTION100
2.3841-2.4610.2911330.22553509X-RAY DIFFRACTION100
2.461-2.5490.27241440.21853524X-RAY DIFFRACTION100
2.549-2.65110.2571470.20713523X-RAY DIFFRACTION100
2.6511-2.77170.2411380.20783535X-RAY DIFFRACTION100
2.7717-2.91780.25671460.20233533X-RAY DIFFRACTION100
2.9178-3.10060.27661450.19673519X-RAY DIFFRACTION100
3.1006-3.340.27461410.19173516X-RAY DIFFRACTION100
3.34-3.6760.22951450.16453553X-RAY DIFFRACTION100
3.676-4.20780.16761430.14013561X-RAY DIFFRACTION100
4.2078-5.30050.14061410.13453559X-RAY DIFFRACTION100
5.3005-52.65930.16881430.15473609X-RAY DIFFRACTION99
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)
15.5615-2.2841-1.36894.00132.28971.7869-0.0901-0.27890.11870.31570.22770.0404-0.10130.1132-0.13980.2228-0.0119-0.01980.2033-0.00490.2831-9.371918.88831.8331
29.20891.0915-0.29727.0568-0.58623.1589-0.162-1.16780.71090.96070.0534-0.018-0.01980.37990.10660.45040.0422-0.04770.5022-0.07760.3466-7.820522.644813.6898
33.77-0.7811-1.763.63862.04134.79280.0692-0.43040.49060.15620.0959-0.2982-0.45540.7864-0.21560.2884-0.10090.00820.3790.00360.41422.045722.5138-4.1393
41.7765-0.3045-0.35141.01-0.03512.05920.0022-0.00580.09850.0282-0.02-0.1464-0.04260.17690.02590.2045-0.01570.01370.18070.01210.2411-7.644311.8288-7.6107
52.9108-1.2128-0.35645.14940.89042.3085-0.0307-0.3715-0.02220.64370.0728-0.08310.19280.0937-0.03910.2842-0.01860.0210.2570.02920.2708-19.4233.98830.7034
62.7035-0.4664-2.04312.565-1.21593.4924-0.0570.21740.1676-0.25020.02210.1868-0.1312-0.360.06470.23670.0027-0.01680.2470.02150.2963-32.122517.5749-7.7072
73.0055-1.8871-2.28447.27393.2274.3103-0.27940.0584-0.39110.0019-0.19310.64070.2082-0.42350.42570.25950.00230.04240.2370.0120.2762-34.53999.24622.1026
80.9009-0.4684-1.20631.82991.0652.9268-0.09670.02610.02350.05690.07980.10220.0304-0.02860.01670.2120.0104-0.02810.24440.01150.2986-23.61138.9078-8.1594
96.93512.7086-4.34953.6667-1.85335.1944-0.26290.3557-0.5902-0.17210.1185-0.2720.58130.02730.17440.36980.04580.01860.2521-0.02220.3061-7.2611-1.4184-21.0883
103.7488-1.33970.50315.8662.07983.7290.0719-0.80390.49310.3850.0525-0.0716-1.12050.2592-0.10710.6761-0.21230.16120.6086-0.17450.485312.038937.3318-26.7022
116.1544-1.76241.13387.4507-1.92742.43050.5081-0.20621.28680.4395-0.3084-0.4505-1.43160.8948-0.28350.8212-0.35360.23980.7816-0.14360.738523.667938.2427-35.7591
122.7702-0.3408-0.2192.89030.17952.35110.2028-0.61820.20890.291-0.0166-0.4774-0.3751.0704-0.15360.3731-0.13620.04810.787-0.05210.416924.443823.8617-34.4252
133.6059-1.1878-1.18092.422-0.16112.97490.1948-0.05520.1239-0.2097-0.0580.0277-0.36350.2416-0.13170.3544-0.06560.10010.3052-0.07070.30829.879126.6731-44.8372
142.75652.72050.35395.3998-1.89312.81620.158-0.5530.17360.2074-0.19940.088-0.20910.19990.08890.2776-0.02120.08160.451-0.01260.30292.726620.9732-28.6179
153.88470.66840.03931.605-0.31154.2620.046-0.12970.51940.01580.00350.2486-0.7573-0.5392-0.03910.51020.08410.09110.36070.01840.3932-7.173329.3112-40.263
163.2248-0.4479-0.81296.1509-0.73253.55070.1523-0.00540.24640.6683-0.07730.6964-0.3273-0.7233-0.00480.39210.09650.07130.53240.00850.3991-11.769825.467-33.6355
173.63450.5559-2.52750.1902-0.77523.8436-0.06780.3082-0.1633-0.2361-0.0974-0.06440.0281-0.30680.17720.3470.00180.03270.3267-0.00690.30876.503617.5013-50.5807
187.352-0.9247-1.84282.47570.6684.0699-0.15930.8185-0.4083-0.3485-0.1004-0.12870.41540.02980.34530.47010.07180.0570.3312-0.01680.316314.546810.1477-49.5866
191.71011.7568-0.93347.42950.94456.8895-0.2047-0.1627-0.6716-0.63460.1245-0.10520.04960.7070.08140.71730.15620.16450.67610.08720.85122.54116.5142-42.3503
205.6456-1.4019-6.65465.15850.99288.0776-1.2338-2.7005-0.29320.83830.50110.29110.40880.58040.76730.78660.25360.04271.022-0.05510.731313.6885.724-32.2358
217.19434.21680.94438.0576-0.80713.6278-0.4712-1.1335-0.99380.96780.4091-0.04231.1330.80360.06180.4150.1066-0.03130.46030.09370.375137.454815.7861-72.1198
223.6313-2.2591-5.32055.70022.9488.1609-0.0121-0.82540.4744-0.15450.2597-0.7037-0.82920.8481-0.2630.5138-0.01050.00410.5459-0.07070.588140.452623.8091-76.2651
236.7611-0.8561-2.37644.37520.77144.9191-0.0867-0.41250.04610.3719-0.0382-0.07250.0840.21950.11030.33220.04270.01660.2593-0.0150.192629.807919.2512-75.5517
245.67890.336-4.19261.812-0.06938.2774-0.11120.3193-0.09660.0558-0.16460.30230.1057-0.8070.2660.34710.03410.04940.3928-0.09310.289316.816418.5324-73.041
257.0578-3.08133.02314.20430.01633.98240.01470.79720.4421-0.4183-0.56360.3822-0.7002-1.53860.58680.50520.173-0.06960.7919-0.13240.32678.227426.2087-73.8943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 243 )
5X-RAY DIFFRACTION5chain 'A' and (resid 244 through 273 )
6X-RAY DIFFRACTION6chain 'A' and (resid 274 through 311 )
7X-RAY DIFFRACTION7chain 'A' and (resid 312 through 338 )
8X-RAY DIFFRACTION8chain 'A' and (resid 339 through 401 )
9X-RAY DIFFRACTION9chain 'A' and (resid 402 through 438 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 64 )
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 88 )
12X-RAY DIFFRACTION12chain 'B' and (resid 89 through 160 )
13X-RAY DIFFRACTION13chain 'B' and (resid 161 through 238 )
14X-RAY DIFFRACTION14chain 'B' and (resid 239 through 268 )
15X-RAY DIFFRACTION15chain 'B' and (resid 269 through 324 )
16X-RAY DIFFRACTION16chain 'B' and (resid 325 through 373 )
17X-RAY DIFFRACTION17chain 'B' and (resid 374 through 401 )
18X-RAY DIFFRACTION18chain 'B' and (resid 402 through 440 )
19X-RAY DIFFRACTION19chain 'D' and (resid 373 through 379 )
20X-RAY DIFFRACTION20chain 'D' and (resid 380 through 385 )
21X-RAY DIFFRACTION21chain 'F' and (resid 13 through 24 )
22X-RAY DIFFRACTION22chain 'F' and (resid 25 through 36 )
23X-RAY DIFFRACTION23chain 'F' and (resid 37 through 69 )
24X-RAY DIFFRACTION24chain 'F' and (resid 70 through 125 )
25X-RAY DIFFRACTION25chain 'F' and (resid 126 through 139 )

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