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- PDB-7q1f: CPAP:TUBULIN:IE5 ALPHAREP COMPLEX -

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Basic information

Entry
Database: PDB / ID: 7q1f
TitleCPAP:TUBULIN:IE5 ALPHAREP COMPLEX
Components
  • Centromere protein J
  • IE5 ALPHAREP
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / MICROTUBULE / CENTROMERE PROTEIN J / CENTRIOLE
Function / homology
Function and homology information


microtubule-based process / structural constituent of cytoskeleton / microtubule / GTP binding / cytoplasm
Similarity search - Function
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/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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha chain
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.347 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 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _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
D: IE5 ALPHAREP
P: Centromere protein J
R: Tubulin alpha chain
S: Tubulin beta chain
T: IE5 ALPHAREP
U: IE5 ALPHAREP
V: Centromere protein J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,46123
Polymers318,31710
Non-polymers3,14413
Water12,827712
1
A: Tubulin alpha chain
B: Tubulin beta chain
C: IE5 ALPHAREP
D: IE5 ALPHAREP
P: Centromere protein J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,82512
Polymers159,1595
Non-polymers1,6667
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
R: Tubulin alpha chain
S: Tubulin beta chain
T: IE5 ALPHAREP
U: IE5 ALPHAREP
V: Centromere protein J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,63611
Polymers159,1595
Non-polymers1,4776
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.088, 215.864, 95.536
Angle α, β, γ (deg.)90, 109.61, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 10 molecules ARBSCDTUPV

#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.: 4
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


Mass: 8606.816 Da / Num. of mol.: 2
Mutation: V319M, A320V, A361del, E362del, P364G, L365G, P366G, I367G, K368del, A369del
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)

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Non-polymers , 7 types, 725 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: 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
#9: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.8
Details: 0.18 M tri-ammonium citrate, 0.1 M Mes-K pH 6.8, 18.5 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.347→107.932 Å / Num. obs: 97303 / % possible obs: 90.8 % / Redundancy: 7.2 % / CC1/2: 0.994 / Rpim(I) all: 0.07 / Rrim(I) all: 0.189 / Net I/σ(I): 7.1
Reflection shellResolution: 2.347→2.609 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4866 / CC1/2: 0.675 / Rpim(I) all: 0.415 / Rrim(I) all: 1.107

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Processing

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

6gwc


Resolution: 2.347→107.93 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.562 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.526 / SU Rfree Blow DPI: 0.26 / SU Rfree Cruickshank DPI: 0.266
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 4793 -RANDOM
Rwork0.1881 ---
obs0.1897 97303 68.8 %-
Displacement parametersBiso mean: 65.63 Å2
Baniso -1Baniso -2Baniso -3
1--1.475 Å20 Å2-0.935 Å2
2--6.9767 Å20 Å2
3----5.5017 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.347→107.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19345 0 193 712 20250
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00819970HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9627168HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6856SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3509HARMONIC5
X-RAY DIFFRACTIONt_it19891HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2670SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact16515SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion19.18
LS refinement shellResolution: 2.35→2.51 Å
RfactorNum. reflection% reflection
Rfree0.2258 111 -
Rwork0.2197 --
obs0.2201 1947 7.73 %
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)
11.1151-0.39840.33831.4441-0.38691.20850.0037-0.0015-0.1181-0.00150.014-0.0368-0.1181-0.0368-0.0177-0.13840.0005-0.00430.0302-0.0209-0.1468-35.2493-50.659661.5359
21.9616-0.456-0.37122.02820.1041.8124-0.0670.00960.26270.0096-0.0004-0.08880.2627-0.08880.0674-0.1209-0.0391-0.0165-0.1004-0.0234-0.2175-19.3249-88.874669.2761
32.76-2.1424-0.50162.8057-0.36662.9383-0.06880.33740.69270.3374-0.0883-0.05220.6927-0.05220.15710.069-0.07920.0509-0.06770.1739-0.1035-13.221-101.1881.9363
41.4153-0.15220.6613.847-3.44485.6668-0.2080.754-0.91630.7540.2018-0.1719-0.9163-0.17190.0062-0.15480.0571-0.0011-0.2764-0.068-0.0711-43.2878-20.231162.3385
55.7821.74051.98190.17371.57386.29510.0788-0.00740.062-0.0074-0.03070.90480.0620.9048-0.0481-0.430.1537-0.0118-0.0711-0.20750.09718.2789-96.493271.329
60.83020.22970.33341.24920.69051.82680.02950.05460.19020.0546-0.0496-0.07480.1902-0.07480.0201-0.09220.0242-0.0050.02660.0222-0.19257.0757-60.967427.9274
72.97070.3775-0.34831.91840.02522.00780.1920.0472-0.35370.0472-0.0525-0.0592-0.3537-0.0592-0.1395-0.24240.01780.0232-0.27230.0288-0.00087.7491-22.236644.5607
83.50642.18491.67814.26471.44292.63890.08430.42620.7220.42620.23210.08180.7220.0818-0.3164-0.04990.0828-0.0089-0.2944-0.0064-0.210311.3825-91.871820.8305
92.38731.83491.546201.5157.9842-0.0390.1985-0.24340.1985-0.3506-0.179-0.2434-0.1790.3897-0.39340.19170.2460.0374-0.2544-0.0348-7.0426-13.593679.598
100.8142-0.0182-0.53192.46811.79321.79030.04420.3466-0.39960.34660.01620.2526-0.39960.2526-0.0604-0.1842-0.19240.0053-0.0428-0.08940.029217.453-10.849256.1567
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ P|* }
4X-RAY DIFFRACTION4{ C|* }
5X-RAY DIFFRACTION5{ D|* }
6X-RAY DIFFRACTION6{ R|* }
7X-RAY DIFFRACTION7{ S|* }
8X-RAY DIFFRACTION8{ T|* }
9X-RAY DIFFRACTION9{ U|* }
10X-RAY DIFFRACTION10{ V|* }

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