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- PDB-4uya: Structure of MLK4 kinase domain with ATPgammaS -

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Basic information

Entry
Database: PDB / ID: 4uya
TitleStructure of MLK4 kinase domain with ATPgammaS
ComponentsMITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE MLK4
KeywordsTRANSFERASE / MIXED-LINEAGE KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / SH3 DOMAIN / LEUCINE ZIPPER 1
Function / homology
Function and homology information


: / mitogen-activated protein kinase kinase kinase / MAP kinase kinase kinase activity / protein autophosphorylation / protein kinase activity / protein phosphorylation / signal transduction / protein homodimerization activity / ATP binding / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase kinase kinase 21
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRead, J.A. / Brassington, C. / Pollard, H.K. / Phillips, C. / Green, I. / Overmann, R. / Collier, M.
CitationJournal: Cancer Res. / Year: 2016
Title: Recurrent Mlk4 Loss-of-Function Mutations Suppress Jnk Signaling to Promote Colon Tumorigenesis.
Authors: Marusiak, A.A. / Stephenson, N.L. / Baik, H. / Trotter, E.W. / Li, Y. / Blyth, K. / Mason, S. / Chapman, P. / Puto, L.A. / Read, J.A. / Brassington, C. / Pollard, H.K. / Phillips, C. / ...Authors: Marusiak, A.A. / Stephenson, N.L. / Baik, H. / Trotter, E.W. / Li, Y. / Blyth, K. / Mason, S. / Chapman, P. / Puto, L.A. / Read, J.A. / Brassington, C. / Pollard, H.K. / Phillips, C. / Green, I. / Overman, R. / Collier, M. / Testoni, E. / Miller, C. / Hunter, T. / Sansom, O.J. / Brognard, J.
History
DepositionAug 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE MLK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0454
Polymers38,4731
Non-polymers5723
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.011, 35.163, 70.022
Angle α, β, γ (deg.)90.00, 96.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE MLK4 / MIXED LINEAGE KINASE 4


Mass: 38473.230 Da / Num. of mol.: 1
Fragment: KINASE DOMAIN WITH N-TERMINAL LEUCINE ZIPPER 1, UNP RESIDUES 115-451
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PROTEIN DEPHOSPHORYLATED / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q5TCX8, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER (AGS): ALSO KNOWN AS ATPGAMMAS
Sequence detailsA214G AND LOOP DELETION OF 215-229 TO REMOVE KINASE INSERT DOMAIN S303A AND T307A TO PREVENT ...A214G AND LOOP DELETION OF 215-229 TO REMOVE KINASE INSERT DOMAIN S303A AND T307A TO PREVENT ACTIVATION LOOP PHOSPHORYLATION

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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: 2.37 Å3/Da / Density % sol: 47.71 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→56 Å / Num. obs: 6917 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 102.64 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.6
Reflection shellResolution: 2.8→3.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DTC

3dtc


Resolution: 2.8→56.16 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.8712 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.397
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 353 5.11 %RANDOM
Rwork0.2011 ---
obs0.2043 6903 98.68 %-
Displacement parametersBiso mean: 82.07 Å2
Baniso -1Baniso -2Baniso -3
1-17.0133 Å20 Å211.6424 Å2
2---1.8682 Å20 Å2
3----15.1451 Å2
Refine analyzeLuzzati coordinate error obs: 0.397 Å
Refinement stepCycle: LAST / Resolution: 2.8→56.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 33 39 2083
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092090HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.152859HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d652SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes32HARMONIC2
X-RAY DIFFRACTIONt_gen_planes308HARMONIC5
X-RAY DIFFRACTIONt_it2090HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion24.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion284SEMIHARMONIC5
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_contact2357SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.13 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3599 98 5.1 %
Rwork0.2355 1823 -
all0.2418 1921 -
obs--98.68 %
Refinement TLS params.Method: refined / Origin x: 16.6583 Å / Origin y: 0.0219 Å / Origin z: 18.6332 Å
111213212223313233
T-0.1272 Å20.0317 Å20.0543 Å2--0.2559 Å2-0.061 Å2---0.3692 Å2
L7.8609 °22.017 °21.067 °2-1.6333 °20.4806 °2--0.9634 °2
S-0.1007 Å °-0.6814 Å °0.3813 Å °-0.0408 Å °-0.0153 Å °-0.1127 Å °-0.1775 Å °0.0563 Å °0.116 Å °
Refinement TLS groupSelection details: CHAIN A

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