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- PDB-7z0f: CPAP:S-TUBULIN:IIH5 ALPHAREP COMPLEX -

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Basic information

Entry
Database: PDB / ID: 7z0f
TitleCPAP:S-TUBULIN:IIH5 ALPHAREP COMPLEX
Components
  • Centromere protein J
  • IIH5 ALPHAREP
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / MICROTUBULE / VINCA DOMAIN INHIBITORS / CENTRIOLE
Function / homology
Function and homology information


astral microtubule nucleation / centriole elongation / gamma-tubulin small complex / positive regulation of centriole elongation / positive regulation of non-motile cilium assembly / positive regulation of establishment of protein localization / regulation of centriole replication / procentriole replication complex / 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 non-motile cilium assembly / positive regulation of establishment of protein localization / regulation of centriole replication / procentriole replication complex / 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 / microtubule-based process / centriole replication / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / 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 / protein domain specific binding / cell division / centrosome / GTP binding / protein kinase binding / identical protein binding / cytoplasm / cytosol
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'-DIPHOSPHATE / 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: 2.396 Å
AuthorsGigant, B. / Campanacci, V.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation ARC 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
DepositionFeb 22, 2022Deposition 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
P: Centromere protein J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3538
Polymers128,2714
Non-polymers1,0834
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-54 kcal/mol
Surface area40000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.28, 86.71, 137.61
Angle α, β, γ (deg.)90, 96.61, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ABCP

#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.: 1
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: 9199.604 Da / Num. of mol.: 1 / Mutation: V319M, A320V
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 , 5 types, 163 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-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


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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Na tartrate, 10% (W/V) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.396→45.79 Å / Num. obs: 49614 / % possible obs: 99.19 % / Redundancy: 4.47 % / CC1/2: 0.998 / Rpim(I) all: 0.054 / Rrim(I) all: 0.083 / Net I/σ(I): 13.06
Reflection shellResolution: 2.396→2.482 Å / Redundancy: 4.51 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 4790 / CC1/2: 0.62 / Rrim(I) all: 1.556 / % possible all: 95.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GWD

6gwd


Resolution: 2.396→45.79 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.345 / SU Rfree Blow DPI: 0.256 / SU Rfree Cruickshank DPI: 0.263
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 2481 -RANDOM
Rwork0.2215 ---
obs0.224 49614 99.2 %-
Displacement parametersBiso mean: 99.87 Å2
Baniso -1Baniso -2Baniso -3
1-6.0156 Å20 Å2-9.786 Å2
2--1.8719 Å20 Å2
3----7.8876 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.396→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7840 0 67 159 8066
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088063HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9910984HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2653SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1425HARMONIC5
X-RAY DIFFRACTIONt_it8063HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1099SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6102SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion19.25
LS refinement shellResolution: 2.4→2.42 Å
RfactorNum. reflection% reflection
Rfree0.4866 50 -
Rwork0.4291 --
obs0.4319 993 82.47 %
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)
11.72480.0126-0.36760.74020.24821.6272-0.168-0.1109-0.2045-0.11090.04190.1313-0.20450.13130.1261-0.0834-0.04730.0878-0.3092-0.04930.4051-15.0611-0.1194-13.5522
23.21460.5162-1.11410.8363-0.19072.36360.4143-0.4136-0.5058-0.4136-0.1517-0.3925-0.5058-0.3925-0.26260.32070.13120.26210.2396-0.1232-0.3433-11.83313.6326-52.5659
3-0.05641.3412-0.00040-1.15914.2055-0.3901-0.0890.5718-0.0890.25710.17790.57180.17790.1329-0.0188-0.03820.33840.5387-0.3098-0.2416-10.50727.2676-71.8158
47.6731-1.6694-0.41190.8817-0.13990.2383-0.2556-0.0238-0.2528-0.02380.10970.0525-0.25280.05250.1459-0.13580.04490.0784-0.04960.2790.2743-1.27890.314120.1903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 438
2X-RAY DIFFRACTION1{ A|* }A600 - 601
3X-RAY DIFFRACTION1{ A|* }A602 - 605
4X-RAY DIFFRACTION2{ B|* }B2 - 441
5X-RAY DIFFRACTION2{ B|* }B600
6X-RAY DIFFRACTION3{ P|* }P322 - 385
7X-RAY DIFFRACTION4{ C|* }C14 - 170
8X-RAY DIFFRACTION4{ C|* }C500

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