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- PDB-2npt: Crystal Structure of the complex of human mitogen activated prote... -

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Basic information

Entry
Database: PDB / ID: 2npt
TitleCrystal Structure of the complex of human mitogen activated protein kinase kinase 5 phox domain (MAP2K5-phox) with human mitogen activated protein kinase kinase kinase 2 phox domain (MAP3K2-phox)
Components
  • Dual specificity mitogen-activated protein kinase kinase 5
  • Mitogen-activated protein kinase kinase kinase 2
KeywordsTRANSFERASE / mitogen activated protein kinase kinase 5 / MAP2K5 / MEK5 / MKK5 / PRKMK5 / MAP kinase kinase 5 / phox / phox-domain / mitogen activated protein kinase kinase kinase 2 / MAP3K2 / MAPK/ERK kinase kinase 2 / MAPKKK2 / MEK kinase 2 / MEKK2 / MEKK2B / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ERK5 cascade / Signalling to ERK5 / negative regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / mitogen-activated protein kinase kinase kinase / negative regulation of interleukin-8 production / mitogen-activated protein kinase kinase / cellular response to laminar fluid shear stress / negative regulation of cell migration involved in sprouting angiogenesis ...ERK5 cascade / Signalling to ERK5 / negative regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / mitogen-activated protein kinase kinase kinase / negative regulation of interleukin-8 production / mitogen-activated protein kinase kinase / cellular response to laminar fluid shear stress / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / negative regulation of smooth muscle cell apoptotic process / MAP kinase kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / MAP kinase kinase kinase activity / positive regulation of protein metabolic process / : / insulin-like growth factor receptor signaling pathway / positive regulation of epithelial cell proliferation / positive regulation of MAP kinase activity / cellular response to growth factor stimulus / spindle / cellular response to mechanical stimulus / MAPK cascade / heart development / positive regulation of cell growth / protein tyrosine kinase activity / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Dual specificity mitogen-activated protein kinase kinase 5, PB1 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) ...Dual specificity mitogen-activated protein kinase kinase 5, PB1 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) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Dual specificity mitogen-activated protein kinase kinase 5 / Mitogen-activated protein kinase kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFilippakopoulos, P. / Debreczeni, J. / Papagrigoriou, V. / Turnbull, A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the complex of human mitogen activated protein kinase kinase 5 phox domain (MAP2K5-phox) with human mitogen activated protein kinase kinase kinase 2 phox domain (MAP3K2-phox)
Authors: Filippakopoulos, P. / Debreczeni, J. / Papagrigoriou, V. / Turnbull, A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Knapp, S.
History
DepositionOct 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 5
B: Mitogen-activated protein kinase kinase kinase 2
C: Dual specificity mitogen-activated protein kinase kinase 5
D: Mitogen-activated protein kinase kinase kinase 2


Theoretical massNumber of molelcules
Total (without water)46,9544
Polymers46,9544
Non-polymers00
Water5,765320
1
A: Dual specificity mitogen-activated protein kinase kinase 5
D: Mitogen-activated protein kinase kinase kinase 2


Theoretical massNumber of molelcules
Total (without water)23,4772
Polymers23,4772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase 2
C: Dual specificity mitogen-activated protein kinase kinase 5


Theoretical massNumber of molelcules
Total (without water)23,4772
Polymers23,4772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.333, 61.410, 143.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 5 / MAP kinase kinase 5 / MAPKK 5 / MAPK/ERK kinase 5


Mass: 11941.498 Da / Num. of mol.: 2 / Fragment: MAP2K5-phox
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K5, MEK5, MKK5, PRKMK5 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-R3
References: UniProt: Q13163, mitogen-activated protein kinase kinase
#2: Protein Mitogen-activated protein kinase kinase kinase 2 / MAPK/ERK kinase kinase 2 / MEK kinase 2 / MEKK 2


Mass: 11535.425 Da / Num. of mol.: 2 / Fragment: MAP3K2-phox
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K2, MAPKKK2, MEKK2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-R3
References: UniProt: Q9Y2U5, mitogen-activated protein kinase kinase kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M NH4(CH3COO), 0.1M TRIS, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 23, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection

Av σ(I) over netI: 7.3 / Number: 282762 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / D res high: 1.407 Å / D res low: 61.43 Å / Num. obs: 42219 / % possible obs: 99.9 / Redundancy: 6.7 %

ID
1
2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.5361.4398.710.0310.0316.2
3.915.5310010.0380.0386.8
3.23.9110010.0490.0496.9
2.773.210010.0490.0496.9
2.472.7710010.070.077
2.262.4710010.1040.1046.9
2.092.2610010.160.167
1.962.0910010.2880.2887
1.841.9610010.4990.4996.9
1.751.8499.510.8760.8765.5
5.5361.4398.720.0310.0316.2
3.915.5310020.0380.0386.8
3.23.9110020.0490.0496.9
2.773.210020.0490.0496.9
2.472.7710020.070.077
2.262.4710020.1040.1046.9
2.092.2610020.160.167
1.962.0910020.2880.2887
1.841.9610020.4990.4996.9
1.751.8499.520.8760.8765.5
ReflectionResolution: 1.75→61.43 Å / Num. all: 42261 / Num. obs: 42219 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 7.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 0.8 / Rsym value: 0.876 / % possible all: 99.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å56.47 Å
Translation3.5 Å56.47 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2CU1, 2C60, 1WI0

2cu1

2c60

1wi0


Resolution: 1.75→32 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.349 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 2038 4.8 %RANDOM
Rwork0.19937 ---
obs0.20166 40100 99.81 %-
all-42218 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.63 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 0 320 3249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223002
X-RAY DIFFRACTIONr_bond_other_d0.0010.022013
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9794072
X-RAY DIFFRACTIONr_angle_other_deg0.97434949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8315376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85624.963135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41615535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3871519
X-RAY DIFFRACTIONr_chiral_restr0.0910.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02557
X-RAY DIFFRACTIONr_nbd_refined0.2070.2525
X-RAY DIFFRACTIONr_nbd_other0.2080.22031
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21409
X-RAY DIFFRACTIONr_nbtor_other0.0860.21634
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1911.51951
X-RAY DIFFRACTIONr_mcbond_other0.2841.5746
X-RAY DIFFRACTIONr_mcangle_it1.85923058
X-RAY DIFFRACTIONr_scbond_it2.73331182
X-RAY DIFFRACTIONr_scangle_it4.0334.51010
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 153 -
Rwork0.294 2853 -
obs--98.33 %
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)
12.50048.58763.058345.332515.27585.34720.0284-0.0337-0.2559-1.15480.6175-0.7002-0.4295-0.2132-0.6459-0.0437-0.0322-0.0105-0.02960.0533-0.013219.393473.769744.0691
21.5843-0.3448-0.14730.49460.18970.63430.0302-0.0306-0.0178-0.07180.038-0.0714-0.008-0.0517-0.0682-0.03010.01150.0048-0.02950.0055-0.008414.818350.909432.0605
30.60720.66730.68811.97280.85651.73150.07120.0667-0.11850.00370.0705-0.03-0.01870.1534-0.1417-0.0372-0.0182-0.0022-0.0161-0.0761-0.02799.107250.1647-11.9921
49.38714.7586-3.80233.70160.31475.4395-0.055-0.3047-0.0848-0.33-0.0780.05160.2320.07080.133-0.0152-0.01070.0162-0.0342-0.0408-0.024230.740874.5604-11.7236
50.4923-0.1135-0.35650.57930.24591.4517-0.04850.02190.01240.02510.0525-0.02110.01790.0059-0.004-0.00870.00040.0054-0.0179-0.0272-0.039311.454267.05773.275
65.7411-4.13991.88973.5378-2.06641.51810.4714-0.03690.04721.1322-0.9419-0.30110.0534-0.50180.47040.0955-0.0273-0.0977-0.0227-0.033-0.01562.614473.502846.4321
70.65180.2449-0.67951.2429-0.08491.6366-0.0267-0.0031-0.04210.0267-0.0866-0.0207-0.0336-0.03610.1133-0.0649-0.011-0.02020.0020.0411-0.015-3.899250.3545.2021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 121 - 10
2X-RAY DIFFRACTION2AA15 - 10813 - 106
3X-RAY DIFFRACTION3BB42 - 12319 - 100
4X-RAY DIFFRACTION4CC3 - 91 - 7
5X-RAY DIFFRACTION5CC10 - 1088 - 106
6X-RAY DIFFRACTION6DD35 - 4212 - 19
7X-RAY DIFFRACTION7DD43 - 12220 - 99

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