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- PDB-6cq7: The SH3 domain of MLK3 in complex with poly-proline peptide deriv... -

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Basic information

Entry
Database: PDB / ID: 6cq7
TitleThe SH3 domain of MLK3 in complex with poly-proline peptide derived from Htt
ComponentsMitogen-activated protein kinase kinase kinase 11, Huntingtin fusion protein
KeywordsTRANSFERASE / Huntington / peptide fusion / mixed lineage kinase 3
Function / homology
Function and homology information


mitogen-activated protein kinase kinase kinase / cell cycle G1/S phase transition / JUN kinase kinase kinase activity / mitogen-activated protein kinase kinase kinase binding / mitogen-activated protein kinase kinase binding / RHOV GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / MAP kinase kinase kinase activity / microtubule-based process ...mitogen-activated protein kinase kinase kinase / cell cycle G1/S phase transition / JUN kinase kinase kinase activity / mitogen-activated protein kinase kinase kinase binding / mitogen-activated protein kinase kinase binding / RHOV GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / MAP kinase kinase kinase activity / microtubule-based process / positive regulation of JUN kinase activity / JNK cascade / positive regulation of JNK cascade / RAF activation / small GTPase binding / positive regulation of neuron apoptotic process / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / microtubule / protein autophosphorylation / protein kinase activity / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein homodimerization activity / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
MLK1-3, SH3 domain / 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 / Serine/threonine-protein kinase, active site ...MLK1-3, SH3 domain / 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 / 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
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKall, S.L. / Lavie, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)NIDCR DE018381 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01EB013685 United States
CitationJournal: To Be Published
Title: The SH3 domain of MLK3 in complex with poly-proline peptide derived from Htt
Authors: Kall, S.L. / Lavie, A.
History
DepositionMar 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 11, Huntingtin fusion protein


Theoretical massNumber of molelcules
Total (without water)8,4341
Polymers8,4341
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mitogen-activated protein kinase kinase kinase 11, Huntingtin fusion protein

A: Mitogen-activated protein kinase kinase kinase 11, Huntingtin fusion protein


Theoretical massNumber of molelcules
Total (without water)16,8682
Polymers16,8682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_564x,-y+1,-z-1/21
Buried area1810 Å2
ΔGint-16 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.000, 59.000, 84.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 11, Huntingtin fusion protein / Mixed lineage kinase 3 / Src-homology 3 domain-containing proline-rich kinase / Mixed lineage ...Mixed lineage kinase 3 / Src-homology 3 domain-containing proline-rich kinase / Mixed lineage kinase 3 / Src-homology 3 domain-containing proline-rich kinase / Huntington disease protein / HD protein


Mass: 8434.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K11, MLK3, PTK1, SPRK, HTT, HD, IT15 / Production host: Escherichia coli (E. coli)
References: UniProt: Q16584, mitogen-activated protein kinase kinase kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.35 Å3/Da / Density % sol: 71.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.5 M Ammonium Sulphate 0.1 M Sodium Citrate pH 5.6 1.1 M Lithium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→59 Å / Num. obs: 10431 / % possible obs: 98.6 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rrim(I) all: 0.04 / Net I/σ(I): 23.56
Reflection shellResolution: 2→2.12 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.46 / CC1/2: 0.843 / Rrim(I) all: 0.674 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
ARP/wARPmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K28

5k28


Resolution: 2→59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.035 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25977 544 5.3 %RANDOM
Rwork0.19625 ---
obs0.19951 9765 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.496 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20 Å2
2--1.73 Å20 Å2
3----3.45 Å2
Refinement stepCycle: 1 / Resolution: 2→59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms542 0 0 30 572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019579
X-RAY DIFFRACTIONr_bond_other_d0.0050.02511
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.957795
X-RAY DIFFRACTIONr_angle_other_deg0.98331188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.313576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66523.70427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0661575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.108155
X-RAY DIFFRACTIONr_chiral_restr0.1140.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021685
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02124
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9235.862301
X-RAY DIFFRACTIONr_mcbond_other4.9265.833300
X-RAY DIFFRACTIONr_mcangle_it6.5638.702378
X-RAY DIFFRACTIONr_mcangle_other6.5558.737379
X-RAY DIFFRACTIONr_scbond_it6.026.292278
X-RAY DIFFRACTIONr_scbond_other6.0146.229276
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.8149.226417
X-RAY DIFFRACTIONr_long_range_B_refined10.60165.093598
X-RAY DIFFRACTIONr_long_range_B_other10.60964.44593
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 40 -
Rwork0.386 678 -
obs--94.72 %

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