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- PDB-2c60: crystal structure of human mitogen-activated protein kinase kinas... -

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Basic information

Entry
Database: PDB / ID: 2c60
Titlecrystal structure of human mitogen-activated protein kinase kinase kinase 3 isoform 2 phox domain at 1.25 A resolution
ComponentsHUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 3 ISOFORM 2
KeywordsTRANSFERASE / MAP3K3 / MAP/ERK KINASE KINASE 3 / MAPKKK3 / MEKK3 / SERINE THREONINE PHOSPHORYLATION / ATP-BINDING / KINASE / MAGNESIUM / METAL-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / positive regulation of p38MAPK cascade / blood vessel development / MAP kinase kinase kinase activity / Interleukin-1 signaling / MAPK cascade / protein autophosphorylation / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity ...mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / positive regulation of p38MAPK cascade / blood vessel development / MAP kinase kinase kinase activity / Interleukin-1 signaling / MAPK cascade / protein autophosphorylation / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsDebreczeni, J.E. / Salah, E. / Papagrigoriou, E. / Burgess, N. / von Delft, F. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of Human Mitogen-Activated Protein Kinase Kinase Kinase 3 Isoform 2 Fox Domain at 1.25 A Resolution
Authors: Debreczeni, J.E. / Salah, E. / Papagrigoriou, E. / Burgess, N. / von Delft, F. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Knapp, S.
History
DepositionNov 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.5May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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_entry_details.has_protein_modification / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 3 ISOFORM 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2763
Polymers13,1441
Non-polymers1322
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.800, 42.300, 30.600
Angle α, β, γ (deg.)90.00, 106.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 3 ISOFORM 2 / MAPK/ERK KINASE KINASE 3 / MEK KINASE 3 / MEKK 3


Mass: 13144.145 Da / Num. of mol.: 1 / Fragment: PHOX DOMAIN, RESIDUES 37-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: Q99759, EC: 2.7.1.37
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPONENT OF A PROTEIN KINASE SIGNAL TRANSDUCTION CASCADE
Has protein modificationY
Sequence detailsTHE FIRST 13 RESIDUES (MHHHHHHSSG VDLGTENLYF QSM) BELONG TO THE HIS-TAG, CLONING ARTIFACT

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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: 2.1 Å3/Da / Density % sol: 42.1 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 150 NANOLITRE SITTING DROPS, 0.2 KSCN, 20% PEG3350, 10% ETHYLENE GLYCOL

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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 22, 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: 1.25→29.32 Å / Num. obs: 26421 / % possible obs: 93.8 % / Observed criterion σ(I): 3 / Redundancy: 5.78 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.81
Reflection shellResolution: 1.25→1.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.25 / % possible all: 88.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHELXDphasing
SHELXEphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: SAD / Resolution: 1.25→39.72 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.719 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1336 5.1 %RANDOM
Rwork0.165 ---
obs0.166 25085 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.53 Å2
2--0.33 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.25→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms676 0 7 128 811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022722
X-RAY DIFFRACTIONr_bond_other_d0.0020.02701
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.987969
X-RAY DIFFRACTIONr_angle_other_deg0.74931626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.312583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65623.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.76715148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.505157
X-RAY DIFFRACTIONr_chiral_restr0.080.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02138
X-RAY DIFFRACTIONr_nbd_refined0.2350.2115
X-RAY DIFFRACTIONr_nbd_other0.1910.2681
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2343
X-RAY DIFFRACTIONr_nbtor_other0.0850.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8471.5450
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4282703
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3513306
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7254.5266
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
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 93
Rwork0.325 1516

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