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- PDB-6gx7: Tubulin-CopN-alphaRep complex -

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Basic information

Entry
Database: PDB / ID: 6gx7
TitleTubulin-CopN-alphaRep complex
Components
  • Low calcium response E
  • Tubulin alpha chain
  • Tubulin beta chain
  • iiiA5 ALPHAREP
KeywordsCELL CYCLE / microtubule / ALPHAREP / COPN
Function / homology
Function and homology information


axonemal microtubule / organelle transport along microtubule / forebrain morphogenesis / cerebellar cortex morphogenesis / protein secretion by the type III secretion system / glial cell differentiation / dentate gyrus development / neuron projection arborization / outer membrane / flagellated sperm motility ...axonemal microtubule / organelle transport along microtubule / forebrain morphogenesis / cerebellar cortex morphogenesis / protein secretion by the type III secretion system / glial cell differentiation / dentate gyrus development / neuron projection arborization / outer membrane / flagellated sperm motility / response to L-glutamate / pyramidal neuron differentiation / centrosome cycle / smoothened signaling pathway / regulation of synapse organization / startle response / motor behavior / response to tumor necrosis factor / locomotory exploration behavior / microtubule polymerization / negative regulation of protein secretion / sperm flagellum / response to mechanical stimulus / microtubule-based process / condensed chromosome / homeostasis of number of cells within a tissue / cellular response to calcium ion / adult locomotory behavior / neuromuscular junction / intracellular protein transport / synapse organization / recycling endosome / cerebral cortex development / visual learning / structural constituent of cytoskeleton / memory / cytoplasmic ribonucleoprotein granule / neuron migration / neuron apoptotic process / gene expression / microtubule / hydrolase activity / protein heterodimerization activity / GTPase activity / GTP binding / protein-containing complex binding / cell surface / metal ion binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / T3SS, Low calcium response E, third helical domain / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...: / T3SS, Low calcium response E, third helical domain / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 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 / Alpha Horseshoe / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / TRIETHYLENE GLYCOL / Tubulin beta chain / Tubulin alpha chain / Low calcium response E
Similarity search - Component
Biological speciessynthetic construct (others)
Chlamydia pneumoniae (bacteria)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsGigant, B. / Campanacci, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Insight into microtubule nucleation from tubulin-capping proteins.
Authors: Campanacci, V. / Urvoas, A. / Cantos-Fernandes, S. / Aumont-Nicaise, M. / Arteni, A.A. / Velours, C. / Valerio-Lepiniec, M. / Dreier, B. / Pluckthun, A. / Pilon, A. / Pous, C. / Minard, P. / Gigant, B.
History
DepositionJun 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3May 22, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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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: Tubulin alpha chain
D: Tubulin beta chain
E: iiiA5 ALPHAREP
F: iiiA5 ALPHAREP
G: Low calcium response E
H: Low calcium response E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,09626
Polymers319,5078
Non-polymers3,58918
Water00
1
A: Tubulin alpha chain
B: Tubulin beta chain
E: iiiA5 ALPHAREP
G: Low calcium response E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,42712
Polymers159,7534
Non-polymers1,6748
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Tubulin alpha chain
D: Tubulin beta chain
F: iiiA5 ALPHAREP
H: Low calcium response E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,66914
Polymers159,7534
Non-polymers1,91610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.060, 95.850, 158.060
Angle α, β, γ (deg.)90.00, 101.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules ACBDEFGH

#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: D0VWZ0
#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: D0VWY9
#3: Protein iiiA5 ALPHAREP


Mass: 22325.449 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 Low calcium response E / Type III secreted protein SctW / Type III secretion regulator YopN/LcrE/InvE/MxiC


Mass: 37223.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia pneumoniae (bacteria)
Gene: lcrE, CP_0433, CPn_0324, BN1224_CV15_B_02610, BN1224_DC9_BL_00250, BN1224_GiD_A_03370, BN1224_H12_DC_00070, BN1224_MUL2216_E_00610, BN1224_Panola_E_01460, BN1224_PB1_B_03230, BN1224_U1271_C_ ...Gene: lcrE, CP_0433, CPn_0324, BN1224_CV15_B_02610, BN1224_DC9_BL_00250, BN1224_GiD_A_03370, BN1224_H12_DC_00070, BN1224_MUL2216_E_00610, BN1224_Panola_E_01460, BN1224_PB1_B_03230, BN1224_U1271_C_01640, BN1224_UZG1_A_03360, BN1224_Wien2_E_01090, BN1224_YK41_BG_00220, CWL029c_C_01640
Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z8L4

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Non-polymers , 6 types, 18 molecules

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


Mass: 523.180 Da / Num. of mol.: 4 / 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.: 4 / 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4

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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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: polyethylene glycol 400, 0.1 M Mes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979346 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979346 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 72103 / % possible obs: 99.1 % / Redundancy: 3.87 % / Biso Wilson estimate: 125.34 Å2 / Rrim(I) all: 0.2023 / Net I/σ(I): 7.37
Reflection shellResolution: 3.19→3.3 Å / Num. unique obs: 6724

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5eyp, 4p40, 3ltm

5eyp

4p40

3ltm


Resolution: 3.19→49.03 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.343
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3606 5 %RANDOM
Rwork0.173 ---
obs0.175 72103 99.2 %-
Displacement parametersBiso mean: 115.1 Å2
Baniso -1Baniso -2Baniso -3
1--9.5161 Å20 Å23.6415 Å2
2--19.8684 Å20 Å2
3----10.3523 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 3.19→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20123 0 218 0 20341
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0120737HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1628211HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7089SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3632HARMONIC5
X-RAY DIFFRACTIONt_it20737HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion22.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2775SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact24860SEMIHARMONIC4
LS refinement shellResolution: 3.19→3.22 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2939 -5.06 %
Rwork0.2788 1370 -
all0.2796 1443 -
obs--71.92 %
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)
11.2690.28010.0043.4533-0.47662.0275-0.04720.374-0.0542-0.390.0673-0.32230.0990.2625-0.0201-0.00820.04250.0154-0.0638-0.0057-0.330359.615-11.651341.0265
21.3854-0.14640.24743.2077-0.14661.71570.1471-0.19040.03260.3185-0.05720.0466-0.0336-0.2303-0.08990.4302-0.0483-0.03370.06080.0194-0.007246.3173-24.789978.4958
31.6147-0.33740.10883.33210.07831.4295-0.02040.09940.015-0.2155-0.0062-0.5809-0.06510.43630.0267-0.1453-0.0101-0.0007-0.10970.0622-0.181935.2299-16.71958.8087
41.2773-0.2920.03573.73450.04491.8788-0.0085-0.0773-0.10060.026-0.06550.2851-0.0644-0.14760.0740.37240.01220.00550.2168-0.03470.2505-4.3118-3.502311.3068
54.46641.80362.45575.61810.45133.1717-0.32950.6080.5493-0.51220.07740.0221-0.45290.60810.25210.14770.1209-0.0666-0.23380.2377-0.371952.973930.633544.4344
62.71260.08382.24816.92772.05975.87010.38150.374-0.40520.15840.0445-0.7690.75920.7354-0.426-0.08590.2352-0.1592-0.31310.1846-0.186730.3015-59.039114.3255
70.76593.29984.91431.33366.60081.96620.12980.5439-0.0986-0.1156-0.17870.029-0.1402-0.33790.04890.1303-0.2359-0.2769-0.0305-0.35710.108211.0093-68.73967.212
85.579-0.8747-1.27876.51265.35536.8644-0.0687-0.1879-1.213-0.2454-0.40650.74270.6514-0.95460.4752-0.423-0.34480.1821-0.16510.1730.235514.4162-49.142687.6459
94.22590.9143-2.43266.96692.135213.8367-0.0505-1.0340.21570.61760.52070.0032-0.62730.7421-0.4701-0.3594-0.18360.23560.2420.1244-0.335421.0405-30.1738110.0527
101.22184.7188-1.2042.14675.48866.21850.002-0.40490.07890.178-0.2304-0.2729-0.18850.57150.22850.0986-0.2376-0.22790.2263-0.3572-0.101-3.804340.354147.9769
116.82752.7171-1.88167.66710.42525.19180.0815-1.15620.52591.04940.18370.2476-0.94680.3251-0.26520.04860.11430.2982-0.0525-0.2842-0.4871-21.929520.771639.9904
1212.50883.20981.68395.62871.61788.51050.08240.9021-0.7607-0.08740.09171.08910.884-0.8367-0.174-0.2261-0.03950.2895-0.139-0.2383-0.068-41.82691.394826.7378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|101 - 172 }
8X-RAY DIFFRACTION8{ G|180 - 275 }
9X-RAY DIFFRACTION9{ G|276 - 383 }
10X-RAY DIFFRACTION10{ H|100 - 172 }
11X-RAY DIFFRACTION11{ H|177 - 275 }
12X-RAY DIFFRACTION12{ H|276 - 383 }

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