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- PDB-6whb: MEKK1 TOG domain (548-867) -

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Basic information

Entry
Database: PDB / ID: 6whb
TitleMEKK1 TOG domain (548-867)
ComponentsMitogen-activated protein kinase kinase kinase 1
KeywordsSIGNALING PROTEIN / Tubulin-binding / localization / protein-binding
Function / homology
Function and homology information


protein serine/threonine kinase activity => GO:0004674 / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / mitogen-activated protein kinase kinase kinase / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / Fc-epsilon receptor signaling pathway / TRAF6 mediated NF-kB activation / MAP kinase kinase kinase activity / FCERI mediated MAPK activation ...protein serine/threonine kinase activity => GO:0004674 / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / mitogen-activated protein kinase kinase kinase / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / Fc-epsilon receptor signaling pathway / TRAF6 mediated NF-kB activation / MAP kinase kinase kinase activity / FCERI mediated MAPK activation / cellular response to mechanical stimulus / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Zinc finger, SWIM-type / Zinc finger SWIM-type profile. / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Zinc finger, SWIM-type / Zinc finger SWIM-type profile. / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Mitogen-activated protein kinase kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.90032055102 Å
AuthorsFilipcik, P. / Mace, P.D.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A cryptic tubulin-binding domain links MEKK1 to curved tubulin protomers.
Authors: Filipcik, P. / Latham, S.L. / Cadell, A.L. / Day, C.L. / Croucher, D.R. / Mace, P.D.
History
DepositionApr 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5379
Polymers37,9651
Non-polymers5728
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, as SEC-MALLS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.817, 71.817, 259.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1056-

HOH

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 1 / MAPK/ERK kinase kinase 1 / MEKK 1


Mass: 37965.492 Da / Num. of mol.: 1 / Fragment: TOG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K1, MAPKKK1, MEKK, MEKK1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q13233, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.1 M Bis-Tris Propane pH 6.9, 1.5 M sodium acetate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX110.9537
SYNCHROTRONAustralian Synchrotron MX121.4586
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDFeb 1, 2016
ADSC QUANTUM 210r2CCDFeb 1, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Si with sagittaly bent second crystalSINGLE WAVELENGTHMx-ray1
2Double Si with sagittaly bent second crystalSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
21.45861
ReflectionResolution: 1.9→47.3 Å / Num. obs: 27403 / % possible obs: 99 % / Redundancy: 28.6 % / Biso Wilson estimate: 44.1557858027 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1447 / Rrim(I) all: 0.1473 / Net I/σ(I): 19.36
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 29 % / Num. unique obs: 2683 / CC1/2: 0.239 / CC star: 0.621 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
Aimless0.5.32data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.90032055102→47.2908101698 Å / SU ML: 0.320125233772 / Cross valid method: FREE R-VALUE / σ(F): 1.32649928869 / Phase error: 28.9789126262
RfactorNum. reflection% reflectionSelection details
Rfree0.229687564641 1381 5.10177694041 %random
Rwork0.2070807354 ---
obs0.208269068866 27069 98.7595315407 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.378466522 Å2
Refinement stepCycle: LAST / Resolution: 1.90032055102→47.2908101698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 38 68 2318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005950226169392284
X-RAY DIFFRACTIONf_angle_d0.7277908456423080
X-RAY DIFFRACTIONf_chiral_restr0.0414032461585367
X-RAY DIFFRACTIONf_plane_restr0.00402486158347386
X-RAY DIFFRACTIONf_dihedral_angle_d16.89864353491391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9004-1.96820.4463073126411130.4151711198952243X-RAY DIFFRACTION87.8121505777
1.9682-2.0470.4005712947361660.33880769822526X-RAY DIFFRACTION100
2.047-2.14020.3001033641441440.2894358796962542X-RAY DIFFRACTION100
2.1402-2.2530.2655758770321320.2547566276382562X-RAY DIFFRACTION100
2.253-2.39420.2678481286031300.2191052771972592X-RAY DIFFRACTION100
2.3942-2.5790.2607406054191220.212371315112580X-RAY DIFFRACTION99.9630040696
2.579-2.83860.2767659291211310.2225271470012600X-RAY DIFFRACTION99.9633967789
2.8386-3.24920.2500529250251540.2103331259442608X-RAY DIFFRACTION100
3.2492-4.09330.1996821651961450.1879288896742633X-RAY DIFFRACTION100
4.0933-47.290.1936012499631440.183507104052802X-RAY DIFFRACTION99.6954314721
Refinement TLS params.Method: refined / Origin x: 34.8197403785 Å / Origin y: 15.2451849573 Å / Origin z: 7.59981569605 Å
111213212223313233
T0.337541809868 Å20.034826493021 Å2-0.0393742900525 Å2-0.230895862252 Å20.0363124634189 Å2--0.309789300445 Å2
L2.87213714246 °2-0.124189667224 °2-1.56610614331 °2-1.55416511577 °20.822182095406 °2--2.73680600704 °2
S0.0079942964481 Å °0.0606343135943 Å °-0.0967580879025 Å °-0.005176568648 Å °0.00489151578313 Å °-0.0676027096401 Å °0.307854564635 Å °-0.0362025943676 Å °-0.0220420589835 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA548 - 867
2X-RAY DIFFRACTION1allA901 - 903
3X-RAY DIFFRACTION1allA904 - 908
4X-RAY DIFFRACTION1allA1001 - 1068

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