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- PDB-3zuv: Crystal structure of a designed selected Ankyrin Repeat protein i... -

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Basic information

Entry
Database: PDB / ID: 3zuv
TitleCrystal structure of a designed selected Ankyrin Repeat protein in complex with the phosphorylated MAP kinase ERK2
Components
  • DESIGNED ANKYRIN REPEAT PROTEIN
  • MITOGEN-ACTIVATED PROTEIN KINASE 1
KeywordsDE NOVO PROTEIN/TRANSFERASE / DE NOVO PROTEIN-TRANSFERASE COMPLEX / ANKYRIN REPEAT PROTEIN / SELECTED BINDER / PROTEIN DESIGN
Function / homology
Function and homology information


phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / Transcriptional and post-translational regulation of MITF-M expression and activity / Negative feedback regulation of MAPK pathway ...phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / Transcriptional and post-translational regulation of MITF-M expression and activity / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / IFNG signaling activates MAPKs / Golgi Cisternae Pericentriolar Stack Reorganization / RHO GTPases Activate WASPs and WAVEs / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Regulation of actin dynamics for phagocytic cup formation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of the apoptosome activity / Signaling by Activin / Negative regulation of FGFR2 signaling / Signal transduction by L1 / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interferon gamma signaling / FCERI mediated MAPK activation / Regulation of HSF1-mediated heat shock response / diadenosine tetraphosphate biosynthetic process / MAP2K and MAPK activation / neural crest cell development / Recycling pathway of L1 / cellular response to toxic substance / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / mitogen-activated protein kinase kinase kinase binding / cellular response to methionine / response to epidermal growth factor / positive regulation of macrophage proliferation / response to alcohol / regulation of cellular pH / outer ear morphogenesis / regulation of Golgi inheritance / labyrinthine layer blood vessel development / RAF/MAP kinase cascade / Thrombin signalling through proteinase activated receptors (PARs) / ERBB signaling pathway / Neutrophil degranulation / mammary gland epithelial cell proliferation / trachea formation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / cellular response to insulin-like growth factor stimulus / ERBB2-ERBB3 signaling pathway / positive regulation of macrophage chemotaxis / regulation of cytoskeleton organization / response to exogenous dsRNA / face development / lung morphogenesis / positive regulation of telomere maintenance / response to testosterone / pseudopodium / Bergmann glial cell differentiation / androgen receptor signaling pathway / thyroid gland development / steroid hormone receptor signaling pathway / decidualization / MAP kinase activity / negative regulation of cell differentiation / regulation of ossification / JUN kinase activity / mitogen-activated protein kinase / phosphatase binding / Schwann cell development / progesterone receptor signaling pathway / stress-activated MAPK cascade / estrous cycle / positive regulation of cardiac muscle cell proliferation / cellular response to platelet-derived growth factor stimulus / cellular response to cAMP / sensory perception of pain / dendrite cytoplasm / phosphotyrosine residue binding / myelination / RNA polymerase II CTD heptapeptide repeat kinase activity / peptidyl-threonine phosphorylation / ERK1 and ERK2 cascade / cellular response to epidermal growth factor stimulus
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Ankyrin repeat-containing domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Ankyrin repeat-containing domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsKummer, L. / Mittl, P.R. / Pluckthun, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and Functional Analysis of Phosphorylation-Specific Binders of the Kinase Erk from Designed Ankyrin Repeat Protein Libraries.
Authors: Kummer, L. / Parizek, P. / Rube, P. / Millgramm, B. / Prinz, A. / Mittl, P.R. / Kaufholz, M. / Zimmermann, B. / Herberg, F.W. / Pluckthun, A.
History
DepositionJul 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MITOGEN-ACTIVATED PROTEIN KINASE 1
B: DESIGNED ANKYRIN REPEAT PROTEIN
C: MITOGEN-ACTIVATED PROTEIN KINASE 1
D: DESIGNED ANKYRIN REPEAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3306
Polymers114,1384
Non-polymers1922
Water3,657203
1
A: MITOGEN-ACTIVATED PROTEIN KINASE 1
B: DESIGNED ANKYRIN REPEAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1653
Polymers57,0692
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-21.1 kcal/mol
Surface area23110 Å2
MethodPISA
2
C: MITOGEN-ACTIVATED PROTEIN KINASE 1
D: DESIGNED ANKYRIN REPEAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1653
Polymers57,0692
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-19.3 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.670, 150.449, 104.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.03643, 0.9983, 0.04652), (-0.9982, 0.03413, 0.04936), (0.04769, -0.004824, 0.9977)25.6918, 28.6722, -27.848
2given(0.05812, 0.9969, 0.05266), (-0.997, 0.05521, 0.0551), (0.05203, -0.0557, 0.9971)23.9008, 28.5893, -28.45

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Components

#1: Protein MITOGEN-ACTIVATED PROTEIN KINASE 1 / MAP KINASE 1 / MAPK 1 / ERT1 / EXTRACELLULAR SIGNAL-REGULATED KINASE 2 / ERK-2 / MAP KINASE ISOFORM ...MAP KINASE 1 / MAPK 1 / ERT1 / EXTRACELLULAR SIGNAL-REGULATED KINASE 2 / ERK-2 / MAP KINASE ISOFORM P42 / P42-MAPK / MITOGEN-ACTIVATED PROTEIN KINASE 2 / MAP KINASE 2 / MAPK 2


Mass: 42319.391 Da / Num. of mol.: 2 / Fragment: RESIDUES 3-358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PETHIS6/MEK1R4F_ERK2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63086, mitogen-activated protein kinase
#2: Protein DESIGNED ANKYRIN REPEAT PROTEIN


Mass: 14749.526 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PDST67_PE59 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.01 Å3/Da / Density % sol: 69.07 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM TRIS-HOAC (PH 7.5), 2 M SODIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0015
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 2, 2010 / Details: MIRRORS
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 2.72→8.12 Å / Num. obs: 84304 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.43
Reflection shellResolution: 2.72→2.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.41 / % possible all: 74.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2ERK, 1MJ0

2erk

1mj0


Resolution: 2.72→77.12 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / SU B: 21.148 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22975 2413 5 %RANDOM
Rwork0.17572 ---
obs0.17837 45852 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.145 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.72→77.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7689 0 10 203 7902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227969
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.97310822
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36824.629391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.1151393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2841546
X-RAY DIFFRACTIONr_chiral_restr0.1280.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216078
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7961.54862
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59227844
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.70533107
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4584.52978
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: 2.717→2.788 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 157 -
Rwork0.263 2979 -
obs--100 %
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)
11.13610.24580.12621.4441-0.39461.60350.0392-0.2197-0.0679-0.0743-0.05490.21510.0489-0.11070.01570.0071-0.008-0.01590.04810.00560.050417.075-20.3303-9.2115
27.5998-0.34360.8261.53180.98144.3771-0.18490.2049-0.13320.04680.1513-0.25530.40860.35230.03360.07410.02240.00990.07010.07250.299135.2429-42.3081-8.1964
31.9036-0.40350.11631.05470.00961.8838-0.11820.0776-0.31070.18960.0781-0.13650.09480.12440.040.1077-0.01350.02620.0333-0.04530.116349.4225-11.16815.6214
43.5943-0.7347-0.89556.28880.10194.86080.10210.31120.9895-0.08370.2028-0.6572-0.6910.4437-0.30480.2037-0.16980.08230.2269-0.08440.647872.32746.419317.094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 358
2X-RAY DIFFRACTION2B13 - 134
3X-RAY DIFFRACTION3C0 - 358
4X-RAY DIFFRACTION4D12 - 133

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