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- PDB-7qro: Crystal structure of the unconventional kinetochore protein Trypa... -

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Basic information

Entry
Database: PDB / ID: 7qro
TitleCrystal structure of the unconventional kinetochore protein Trypanosoma brucei KKT4 BRCT domain K543A mutant
ComponentsTrypanosoma brucei KKT4 463-645 K543A
KeywordsCELL CYCLE / kinetochore / kinetoplastids / KKT4 / BRCT
Function / homology
Function and homology information


spindle microtubule / chromosome segregation / kinetochore / microtubule binding / nucleus
Similarity search - Function
BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BRCT domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLudzia, P. / Akiyoshi, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210622/Z/18/Z United Kingdom
Citation
Journal: Biomol.Nmr Assign. / Year: 2024
Title: NMR study of the structure and dynamics of the BRCT domain from the kinetochore protein KKT4.
Authors: Ludzia, P. / Hayashi, H. / Robinson, T. / Akiyoshi, B. / Redfield, C.
#1: Journal: J Cell Biol / Year: 2018
Title: The kinetoplastid kinetochore protein KKT4 is an unconventional microtubule tip-coupling protein.
Authors: Llauro, A. / Hayashi, H. / Bailey, M.E. / Wilson, A. / Ludzia, P. / Asbury, C.L. / Akiyoshi, B.
History
DepositionJan 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypanosoma brucei KKT4 463-645 K543A


Theoretical massNumber of molelcules
Total (without water)19,8551
Polymers19,8551
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Analysis of AUC and SEC-MALS experiments shows that the BRCT domain is monomeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.663, 61.343, 67.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Trypanosoma brucei KKT4 463-645 K543A


Mass: 19854.592 Da / Num. of mol.: 1 / Mutation: K543A
Source method: isolated from a genetically manipulated source
Details: Residues 1-2 (461S, 462M) represent part of a remained linker after TEV protease cleavage.
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.8.3680 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q580Y8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.07 %
Description: Diffraction data were collected 6 months after protein crystals appeared. Crystals appeared as cluster of needles.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: HEPES, sodium chloride, TCEP, sodium thiocyanate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→45.47 Å / Num. obs: 18591 / % possible obs: 99.95 % / Redundancy: 9.7 % / Biso Wilson estimate: 22.17 Å2 / CC1/2: 1 / Rrim(I) all: 0.048 / Net I/σ(I): 1.43
Reflection shellResolution: 1.8→1.89 Å / Num. unique obs: 18590 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZPK

6zpk


Resolution: 1.8→45.47 Å / SU ML: 0.1578 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 21.3175
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2308 860 4.63 %
Rwork0.1963 17731 -
obs0.1978 18591 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.24 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 0 171 1388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891241
X-RAY DIFFRACTIONf_angle_d1.08311683
X-RAY DIFFRACTIONf_chiral_restr0.0651194
X-RAY DIFFRACTIONf_plane_restr0.0068217
X-RAY DIFFRACTIONf_dihedral_angle_d20.031466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.910.2181360.19642886X-RAY DIFFRACTION99.93
1.91-2.060.1971290.20382922X-RAY DIFFRACTION100
2.06-2.270.23321580.19412906X-RAY DIFFRACTION99.97
2.27-2.60.22631370.20652947X-RAY DIFFRACTION100
2.6-3.270.23541530.20572960X-RAY DIFFRACTION100
3.27-45.470.23871470.18633110X-RAY DIFFRACTION99.82
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)
13.4881878672-1.83869601322-4.399120189014.950695987412.05605314438.00653922495-0.19467512133-0.3445890680890.07012934984090.4538970705170.20603527707-0.1391487730550.3643242561050.3424317887120.02496722937370.233683797860.0661654282070.01644346334610.2647435279250.04694293428710.18844867359920.39588721753.3446675859721.6943759023
25.321383996450.4269470410721.353102263593.16450039446-0.1784912690714.082055182740.06667584266580.4947758082870.493483146984-0.908370342324-0.06940274039660.329862542125-0.6432709603680.2232593447990.01201011837550.4031884566780.03150620784950.04426513589620.1745925134190.02391554362120.25956708852620.82646164419.351800406773.44855180341
32.76887715884-0.373287084818-1.994831608275.633383545951.315322198681.647341918640.07823827533870.2835246781820.263487813051-1.02259513330.0250396284633-0.331345278175-0.1570905006480.3236043028410.02247465677380.3417360699180.05501504525480.04202647086820.2562539239610.05453886114660.20883437510127.78837448871.871322972052.69903815579
41.08916967110.442188532120.6549786144013.897625195132.109294072982.190408346290.04289114838950.005041729500910.0479052569087-0.0845901029528-0.05668906592320.0206076890988-0.08717045162750.04044011495250.02503964264690.1381286879630.0205180572440.00386074822960.139644090613-0.006231166818210.13750432375217.8406584527-2.308721018388.68507037208
54.547677042980.4756453707972.126334094533.894209121010.6301878816963.291339175890.1785863041390.250935323983-0.343871356665-0.1581887043640.140609367608-0.3307465744660.3625726680830.465873256129-0.2267204317410.1913603013510.0328502164912-0.008127435814580.180055487312-0.04596576360660.17025708682614.2209999969-17.0373028685-8.61581690214
64.452649226850.6516603474651.936734662475.163110987710.6831287243924.027641601420.188684600923-0.280512684547-0.4164573217360.2923052697450.01025832428380.04309243107420.585308209035-0.1528872439010.03718755565860.1444887823840.00890857089908-0.03539096285310.14111912044-0.03282715488720.18673165234111.4240000847-18.6635452451-0.202348190799
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 474 through 488 )474 - 4881 - 15
22chain 'A' and (resid 489 through 511 )489 - 51116 - 38
33chain 'A' and (resid 512 through 531 )512 - 53139 - 54
44chain 'A' and (resid 532 through 586 )532 - 58655 - 109
55chain 'A' and (resid 587 through 609 )587 - 609110 - 132
66chain 'A' and (resid 610 through 645 )610 - 645133 - 157

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