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- PDB-7q1e: CPAP:TUBULIN:IIH5 ALPHAREP COMPLEX -

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Basic information

Entry
Database: PDB / ID: 7q1e
TitleCPAP:TUBULIN:IIH5 ALPHAREP COMPLEX
Components
  • Centromere protein J
  • Tubulin alpha chain
  • Tubulin beta chain
  • iiH5 ALPHAREP
KeywordsCELL CYCLE / MICROTUBULE / CENTROMERE PROTEIN J / 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 / 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 / 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 / centriole / tubulin binding / AURKA Activation by TPX2 / ciliary basal body / positive regulation of receptor signaling pathway via JAK-STAT / structural constituent of cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / microtubule / transcription coactivator activity / cell division / protein domain specific binding / centrosome / GTP binding / protein kinase binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
T-complex protein 10, C-terminal domain / T-complex protein 10 family / T-complex protein 10 C-terminus / : / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal ...T-complex protein 10, C-terminal domain / T-complex protein 10 family / T-complex protein 10 C-terminus / : / 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
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha chain / Centromere protein J
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCampanacci, V. / Gigant, b.
Funding support France, 2items
OrganizationGrant numberCountry
Fondation ARC France
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural convergence for tubulin binding of CPAP and vinca domain microtubule inhibitors.
Authors: Campanacci, V. / Urvoas, A. / Ammar Khodja, L. / Aumont-Nicaise, M. / Noiray, M. / Lachkar, S. / Curmi, P.A. / Minard, P. / Gigant, B.
History
DepositionOct 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha chain
B: Tubulin beta chain
C: iiH5 ALPHAREP
D: iiH5 ALPHAREP
P: Centromere protein J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,34210
Polymers147,1555
Non-polymers1,1875
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-64 kcal/mol
Surface area47290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.59, 68.05, 420.92
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 5 molecules ABCDP

#1: Protein Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P7DY20
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3TCJ9
#3: Protein iiH5 ALPHAREP


Mass: 18866.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Protein Centromere protein J / / CENP-J / Centrosomal P4.1-associated protein / LAG-3-associated protein / LYST-interacting protein 1


Mass: 9217.643 Da / Num. of mol.: 1 / Mutation: A320V, L342M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPJ, CPAP, LAP, LIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HC77

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Non-polymers , 4 types, 33 molecules

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


Mass: 523.180 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.8 / Details: 8% PEG3350, 0.1M MES-K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→53.6 Å / Num. obs: 43707 / % possible obs: 100 % / Redundancy: 35.6 % / CC1/2: 0.999 / Rrim(I) all: 0.212 / Net I/σ(I): 12.23
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 36.1 % / Num. unique obs: 4416 / CC1/2: 0.339 / Rrim(I) all: 5.39 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GWD

6gwd


Resolution: 2.7→48.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.645 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.645 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.316
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 2186 -RANDOM
Rwork0.1999 ---
obs0.2025 43707 100 %-
Displacement parametersBiso mean: 124.89 Å2
Baniso -1Baniso -2Baniso -3
1-6.1093 Å20 Å20 Å2
2---23.0361 Å20 Å2
3---16.9268 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9200 0 72 28 9300
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099459HARMONIC2
X-RAY DIFFRACTIONt_angle_deg112881HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3165SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1672HARMONIC5
X-RAY DIFFRACTIONt_it9451HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1275SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7457SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion20.03
LS refinement shellResolution: 2.7→2.72 Å
RfactorNum. reflection% reflection
Rfree0.5197 44 -
Rwork0.3404 --
obs0.3493 875 100 %
Refinement TLS params.

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)
14.6649-0.5292-1.26691.21280.88927.7449-0.0718-0.0473-0.1208-0.04730.0691-0.1474-0.1208-0.14740.0027-0.08010.0580.0833-0.2852-0.0766-0.021265.5366-1.6043459.71
23.8668-0.0125-0.83451.54070.84885.91460.13910.1259-0.36450.1259-0.01930.1063-0.36450.1063-0.1198-0.40850.14930.1010.5929-0.2015-0.357661.893612.0409501.16
310.0211.88811.33721.26330.71833.59270.1291-0.2997-0.5492-0.2997-0.258-0.3215-0.5492-0.32150.1289-0.18940.19690.05420.3568-0.1375-0.369952.6421-1.3059426.058
44.948-2.78511.64917.7058-1.7453.1261-0.21390.29581.05480.29580.32290.33951.05480.3395-0.10890.52730.3040.2787-0.5565-0.0149-0.251983.2346-32.8906455.465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* P|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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