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- PDB-7z0g: CPAP:TUBULIN:IE5 ALPHAREP COMPLEX P1 SPACE GROUP -

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Basic information

Entry
Database: PDB / ID: 7z0g
TitleCPAP:TUBULIN:IE5 ALPHAREP COMPLEX P1 SPACE GROUP
Components
  • Centromere protein J
  • IE5 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 establishment of protein localization / positive regulation of non-motile cilium assembly / 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 establishment of protein localization / positive regulation of non-motile cilium assembly / 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 / centriole replication / microtubule polymerization / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / microtubule-based process / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / centriole / Recruitment of mitotic centrosome proteins and complexes / tubulin binding / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic spindle organization / AURKA Activation by TPX2 / 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 / ciliary basal body / protein domain specific binding / cell division / centrosome / protein kinase binding / GTP 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 / : / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / 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 / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 / 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 / Tubulin beta chain / Tubulin alpha chain / Centrosomal P4.1-associated protein
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.487 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: IE5 ALPHAREP
P: Centromere protein J
R: Tubulin alpha chain
S: Tubulin beta chain
T: IE5 ALPHAREP
U: Centromere protein J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,52716
Polymers269,1558
Non-polymers2,3728
Water00
1
A: Tubulin alpha chain
B: Tubulin beta chain
C: IE5 ALPHAREP
P: Centromere protein J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7648
Polymers134,5784
Non-polymers1,1864
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-49 kcal/mol
Surface area39470 Å2
MethodPISA
2
R: Tubulin alpha chain
S: Tubulin beta chain
T: IE5 ALPHAREP
U: Centromere protein J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7648
Polymers134,5784
Non-polymers1,1864
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-50 kcal/mol
Surface area39580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.11, 75.9, 151.32
Angle α, β, γ (deg.)96.19, 98.28, 111.6
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 8 molecules ARBSCTPU

#1: Protein Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3TCJ9
#3: Protein IE5 ALPHAREP


Mass: 25173.736 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: 9199.604 Da / Num. of mol.: 2 / 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 , 4 types, 8 molecules

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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM

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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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Mes-K, 0.2 M Ca acetate, 20% (V/V) polyethylene glycol 400

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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: Sep 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.487→48.54 Å / Num. obs: 28469 / % possible obs: 96.88 % / Redundancy: 3.37 % / CC1/2: 0.982 / Rrim(I) all: 0.272 / Net I/σ(I): 4.96
Reflection shellResolution: 3.487→3.612 Å / Num. unique obs: 2508 / CC1/2: 0.394 / % possible all: 84.36

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Processing

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

6gwc


Resolution: 3.487→48.54 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.857 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.701
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1401 -RANDOM
Rwork0.2365 ---
obs0.2385 28469 97 %-
Displacement parametersBiso mean: 109.74 Å2
Baniso -1Baniso -2Baniso -3
1--5.8903 Å2-0.5191 Å27.0554 Å2
2---7.795 Å222.9052 Å2
3---13.6853 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 3.487→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16327 0 146 0 16473
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00916790HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9822910HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5465SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2963HARMONIC5
X-RAY DIFFRACTIONt_it16638HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2326SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact13574SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion18.88
LS refinement shellResolution: 3.49→3.52 Å
RfactorNum. reflection% reflection
Rfree0.4093 21 -
Rwork0.3536 --
obs0.3557 570 60.17 %
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)
11.2236-0.0928-0.67721.2927-0.88230.7869-0.00750.00350.00230.0035-0.00930.0040.00230.0040.01680.0053-0.00050.0006-0.00120.02640.012-33.2684-16.8254-85.6056
20.5603-0.1278-0.4427-0.11461.62620.8502-0.0005-0.0031-0.0049-0.003100.0014-0.00490.00140.0005-0.01860.00550.01030.0081-0.0331-0.0128-9.7697-41.3994-110.7775
3-0.0024-0.04280.0650.00850.02970.0318-0.00060.0005-0.00040.00050.00060.0003-0.00040.0003-00.0007-0.0001-0.0006-0.0001-0.0022-0.002-1.6768-61.0711-111.5793
40.83510.0078-1.03470.14550.07791.0037-0.003200.001500.0003-0.00650.0015-0.00650.0030.0108-0.00210.0061-0.00760.01490.0061-47.9989-3.7337-61.1656
51.04670.20730.70491.0386-0.66120.7599-0.00310.0027-0.00040.0027-0.01420.0074-0.00040.00740.0173-0.0036-0.00130.00030.00440.02080.0067-33.9154-63.9366-27.4303
60.3981-0.0590.76550.17661.1981.1673-0.0030.00380.00270.0038-0.00030.00190.00270.00190.0033-0.00860.003-0.01130.0049-0.0214-0.009-10.7222-39.6058-2.0411
70.3714-0.11.0850.2084-0.0521.2701-0.00120.0017-0.00160.0017-0.0003-0.0018-0.0016-0.00180.00150.0141-0.0009-0.0094-0.00720.01940.0032-48.6791-76.8847-52.0244
8-0.03160.0320.01090.0406-0.03090.00930.0002-0.0007-0.0002-0.0007-00.0001-0.00020.0001-0.00020.00050.0004-0.00070.0001-0.0003-0.0011-3.0424-20.0638-1.9593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 437
2X-RAY DIFFRACTION1{ A|* }A600 - 601
3X-RAY DIFFRACTION2{ B|* }B2 - 439
4X-RAY DIFFRACTION2{ B|* }B600 - 601
5X-RAY DIFFRACTION3{ P|* }P326 - 386
6X-RAY DIFFRACTION4{ C|* }C12 - 229
7X-RAY DIFFRACTION5{ R|* }R1 - 437
8X-RAY DIFFRACTION5{ R|* }R600 - 601
9X-RAY DIFFRACTION6{ S|* }S2 - 439
10X-RAY DIFFRACTION6{ S|* }S600 - 601
11X-RAY DIFFRACTION7{ T|* }T11 - 229
12X-RAY DIFFRACTION8{ U|* }U326 - 384

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