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- PDB-5ulm: Structure of the ASK1 central regulatory region -

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Basic information

Entry
Database: PDB / ID: 5ulm
TitleStructure of the ASK1 central regulatory region
ComponentsMitogen-activated protein kinase kinase kinase 5
KeywordsTRANSFERASE / ASK1 / Pleckstrin homology / tetratricopeptide
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 / MAP kinase kinase kinase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / 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 / Oxidative Stress Induced Senescence / neuron apoptotic process / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / external side of plasma membrane / protein phosphorylation / innate immune response / protein serine kinase activity / 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 / cytoplasm / cytosol
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 / Serine/threonine-protein kinase, active site ...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 / 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
Mitogen-activated protein kinase kinase kinase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsMace, P.D. / Kumar, A. / Caradoc-Davies, T.T.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of autoregulatory scaffolding by apoptosis signal-regulating kinase 1.
Authors: Weijman, J.F. / Kumar, A. / Jamieson, S.A. / King, C.M. / Caradoc-Davies, T.T. / Ledgerwood, E.C. / Murphy, J.M. / Mace, P.D.
History
DepositionJan 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 5
B: Mitogen-activated protein kinase kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7423
Polymers90,6502
Non-polymers921
Water6,179343
1
A: Mitogen-activated protein kinase kinase kinase 5


Theoretical massNumber of molelcules
Total (without water)45,3251
Polymers45,3251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4172
Polymers45,3251
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.234, 57.117, 103.575
Angle α, β, γ (deg.)90.00, 104.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 272 - 655 / Label seq-ID: 7 - 390

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSAXS and MALLs data indicate that the biological unit is a monomer

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 5 / Apoptosis signal-regulating kinase 1 / ASK-1 / MAPK/ERK kinase kinase 5 / MEKK 5


Mass: 45324.902 Da / Num. of mol.: 2 / Fragment: unp residues 269-658
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K5, ASK1, MAPKKK5, MEKK5 / Plasmid: pET28 based / Details (production host): LIC modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q99683, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.1 M Sodium Fluoride, 10 % PEG 3350,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→47.1 Å / Num. obs: 49197 / % possible obs: 99.4 % / Redundancy: 5 % / CC1/2: 0.994 / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→47.1 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.668 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.212 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26716 2430 4.9 %RANDOM
Rwork0.23335 ---
obs0.23499 46754 99.72 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 30.648 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å20.31 Å2
2---1.53 Å20 Å2
3----1.37 Å2
Refinement stepCycle: 1 / Resolution: 2.1→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6079 0 6 343 6428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196244
X-RAY DIFFRACTIONr_bond_other_d0.0040.026013
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.958443
X-RAY DIFFRACTIONr_angle_other_deg1.085313820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8595750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42323.862290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.311151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8921534
X-RAY DIFFRACTIONr_chiral_restr0.0860.2956
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026910
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021476
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_it2.391.413001
X-RAY DIFFRACTIONr_mcbond_other2.3861.413000
X-RAY DIFFRACTIONr_mcangle_it3.5972.1023741
X-RAY DIFFRACTIONr_mcangle_other3.5972.1023742
X-RAY DIFFRACTIONr_scbond_it3.1841.693243
X-RAY DIFFRACTIONr_scbond_other3.1821.693243
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6912.4164699
X-RAY DIFFRACTIONr_long_range_B_refined6.77111.9777408
X-RAY DIFFRACTIONr_long_range_B_other6.7711.987409
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 46870 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 163 -
Rwork0.303 3345 -
obs--97.36 %
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)
12.43090.7605-0.67393.9631-1.433.14020.0814-0.332-0.22490.4091-0.0957-0.18090.19420.14020.01430.12440.0014-0.08280.14810.01140.104444.19930.0164.526
21.74820.4853-0.07962.60450.33440.90160.02370.1457-0.0217-0.3668-0.0282-0.0437-0.0367-0.02430.00450.07990.0155-0.02280.07370.0150.043138.19833.50739.239
32.735-0.4344-0.56692.67040.60562.7648-0.03410.1978-0.09050.0412-0.05430.3460.1248-0.22510.08840.0299-0.0157-0.03870.0665-0.01460.13269.74233.87247.367
41.5614-0.02070.17143.86111.79494.34950.0353-0.25950.25120.3431-0.07290.3338-0.2472-0.36180.03760.08910.01080.02580.1779-0.01820.1575-13.86137.871103.214
51.87730.75270.77942.7003-0.16051.3453-0.02390.16090.0143-0.27570.0022-0.11130.00320.09410.02170.0580.027-0.01590.0753-0.01360.0392.97434.33383.068
61.8096-0.08110.30232.6745-0.5023.74240.0170.03190.05390.143-0.0486-0.2639-0.16630.3650.03160.0367-0.0242-0.05640.08370.00950.112323.85933.849104.825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A272 - 385
2X-RAY DIFFRACTION2A386 - 558
3X-RAY DIFFRACTION3A559 - 655
4X-RAY DIFFRACTION4B272 - 378
5X-RAY DIFFRACTION5B379 - 558
6X-RAY DIFFRACTION6B559 - 655

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