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- PDB-2clq: Structure of mitogen-activated protein kinase kinase kinase 5 -

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Basic information

Entry
Database: PDB / ID: 2clq
TitleStructure of mitogen-activated protein kinase kinase kinase 5
ComponentsMITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5
KeywordsTRANSFERASE / METAL-BINDING / APOPTOSIS
Function / homology
Function and homology information


cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress ...cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of cardiac muscle cell apoptotic process / p38MAPK cascade / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / MAP kinase kinase kinase activity / positive regulation of protein kinase activity / positive regulation of myoblast differentiation / stress-activated MAPK cascade / positive regulation of JUN kinase activity / JNK cascade / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to amino acid starvation / response to endoplasmic reticulum stress / response to ischemia / apoptotic signaling pathway / positive regulation of JNK cascade / cellular response to hydrogen peroxide / MAPK cascade / cellular senescence / cellular response to tumor necrosis factor / protein phosphatase binding / neuron apoptotic process / Oxidative Stress Induced Senescence / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / external side of plasma membrane / protein phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / Sterile alpha motif/pointed domain superfamily / Transferase(Phosphotransferase) domain 1 ...MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / Sterile alpha motif/pointed domain superfamily / 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. / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
STAUROSPORINE / Mitogen-activated protein kinase kinase kinase 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBunkoczi, G. / Salah, E. / Fedorov, O. / Pike, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Knapp, S.
CitationJournal: Structure / Year: 2007
Title: Structural and Functional Characterization of the Human Protein Kinase Ask1.
Authors: Bunkoczi, G. / Salah, E. / Filippakopoulos, P. / Fedorov, O. / Muller, S. / Sobott, F. / Parker, S.A. / Zhang, H. / Min, W. / Turk, B.E. / Knapp, S.
History
DepositionApr 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5
B: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3294
Polymers66,3962
Non-polymers9332
Water2,684149
1
A: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5
hetero molecules

A: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3294
Polymers66,3962
Non-polymers9332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area2060 Å2
ΔGint-11.7 kcal/mol
Surface area28270 Å2
MethodPISA
2
B: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5
hetero molecules

B: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3294
Polymers66,3962
Non-polymers9332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2210 Å2
ΔGint-9.6 kcal/mol
Surface area27980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.606, 78.606, 423.279
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A670 - 877
2112B670 - 877
1212A903 - 940
2212B903 - 940
1125A878 - 902
2125B878 - 902

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.84211, -0.53475, -0.07004), (-0.49413, 0.71299, 0.49747), (-0.21608, 0.45353, -0.86465)
Vector: -50.41666, 17.52401, -30.29933)
DetailsTHERE IS CURRENTLY NO BIOCHEMICAL EVIDENCE TO SUPPORT THE OLIGOMERIC STATE INDICATED INREMARK 350 BELOW.

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Components

#1: Protein MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5 / MAP3K5 / MAPK/ERK KINASE KINASE 5 / MEK KINASE 5 / MEKK 5 / APOPTOSIS SIGNAL-REGULATING KINASE 1 / ASK-1


Mass: 33197.887 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN RESIDUES 659-951
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q99683, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.8 Å3/Da / Density % sol: 56.8 % / Description: NONE
Crystal growDetails: 25% PEG3350 0.17M, (NH4)2SO4 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9718
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 2.3→47 Å / Num. obs: 35817 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.7
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL

Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.01 / SU ML: 0.179 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. UNINTERPRETABLE DENSITY NEAR ACTIVE SITE RESIDUES ASP 822 AND PHE 823
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1778 5 %RANDOM
Rwork0.201 ---
obs0.204 33893 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3989 0 70 149 4208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224161
X-RAY DIFFRACTIONr_bond_other_d0.0020.022759
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9955655
X-RAY DIFFRACTIONr_angle_other_deg1.01736758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33625.056178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83615673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1441514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024624
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02808
X-RAY DIFFRACTIONr_nbd_refined0.2150.2852
X-RAY DIFFRACTIONr_nbd_other0.1910.22759
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22065
X-RAY DIFFRACTIONr_nbtor_other0.0920.22173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2143
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.89932644
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.99554128
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.7682071
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.936111527
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11373tight positional0.070.05
11583medium positional0.370.5
2144medium positional0.660.5
2166loose positional1.35
11373tight thermal0.180.5
11583medium thermal1.232
2144medium thermal1.362
2166loose thermal4.6610
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 114
Rwork0.288 2252
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)
14.3564-0.8722.14863.2477-0.74365.0857-0.1656-0.7948-0.17070.56520.25920.27430.0377-0.3492-0.0935-0.11050.17910.1025-0.3105-0.0139-0.2752-0.67080.1921-18.008
22.218-1.58540.33614.74340.13264.4557-0.1352-0.3156-0.15190.28620.14670.2764-0.5428-0.8542-0.0115-0.14750.26320.0507-0.1341-0.0107-0.1833-16.07417.7435-28.5542
33.58390.16281.76263.08950.66424.6368-0.0430.41550.3533-0.8208-0.0044-0.0878-0.70310.57410.04740.06-0.030.0694-0.1874-0.0663-0.2123-48.75058.4545-14.5045
42.14690.3356-0.78986.17851.29855.91710.14530.08450.39230.0377-0.0521-0.3307-1.50290.3632-0.09320.2034-0.20930.015-0.1003-0.136-0.0206-44.192323.55426.3569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A670 - 758
2X-RAY DIFFRACTION2A759 - 940
3X-RAY DIFFRACTION3B670 - 758
4X-RAY DIFFRACTION4B759 - 940

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