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- PDB-6d67: Crystal structure of the human dual specificity phosphatase 1 cat... -

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Basic information

Entry
Database: PDB / ID: 6d67
TitleCrystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion (maltose bound form) in complex with the designed AR protein mbp3_16
Components
  • Designed AR protein mbp3_16
  • Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
KeywordsHYDROLASE / Dual specificity phosphatase / DUSP / C258S / MBP / maltose / DARPin
Function / homology
Function and homology information


negative regulation of meiotic cell cycle / negative regulation of monocyte chemotaxis / endoderm formation / peptidyl-serine dephosphorylation / negative regulation of DNA biosynthetic process / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / regulation of mitotic cell cycle spindle assembly checkpoint / peptidyl-threonine dephosphorylation / negative regulation of p38MAPK cascade ...negative regulation of meiotic cell cycle / negative regulation of monocyte chemotaxis / endoderm formation / peptidyl-serine dephosphorylation / negative regulation of DNA biosynthetic process / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / regulation of mitotic cell cycle spindle assembly checkpoint / peptidyl-threonine dephosphorylation / negative regulation of p38MAPK cascade / RAF-independent MAPK1/3 activation / cellular response to chemokine / negative regulation of cell adhesion / mitogen-activated protein kinase binding / growth factor binding / protein-serine/threonine phosphatase / response to testosterone / detection of maltose stimulus / maltose transport complex / negative regulation of MAP kinase activity / protein serine/threonine phosphatase activity / carbohydrate transport / peptidyl-tyrosine dephosphorylation / response to light stimulus / phosphoprotein phosphatase activity / carbohydrate transmembrane transporter activity / response to cAMP / maltose binding / maltose transport / maltodextrin transmembrane transport / response to retinoic acid / cellular response to hormone stimulus / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of MAPK cascade / protein-tyrosine-phosphatase / ATP-binding cassette (ABC) transporter complex / protein tyrosine phosphatase activity / response to glucocorticoid / cell chemotaxis / response to hydrogen peroxide / response to calcium ion / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / response to estradiol / outer membrane-bounded periplasmic space / periplasmic space / intracellular signal transduction / positive regulation of apoptotic process / negative regulation of cell population proliferation / DNA damage response / negative regulation of apoptotic process / signal transduction / nucleus / membrane / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Ankyrin repeat-containing domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Bacterial extracellular solute-binding protein / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Bacterial extracellular solute-binding protein / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Maltose/maltodextrin-binding periplasmic protein / Dual specificity protein phosphatase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsGumpena, R. / Lountos, G.T. / Waugh, D.S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: MBP-binding DARPins facilitate the crystallization of an MBP fusion protein.
Authors: Gumpena, R. / Lountos, G.T. / Waugh, D.S.
History
DepositionApr 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
B: Designed AR protein mbp3_16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6218
Polymers71,8912
Non-polymers7306
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-4 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.286, 84.699, 105.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1 / MBP / MMBP / Maltodextrin-binding protein / Dual specificity protein phosphatase hVH1 / Mitogen- ...MBP / MMBP / Maltodextrin-binding protein / Dual specificity protein phosphatase hVH1 / Mitogen-activated protein kinase phosphatase 1 / MKP-1 / Protein-tyrosine phosphatase CL100


Mass: 57103.613 Da / Num. of mol.: 1
Mutation: D82A, K83A, E172A, N173A, K239A, E359A, K362A, D363A,D82A, K83A, E172A, N173A, C258S, K239A, E359A, K362A, D363A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, DUSP1, CL100, MKP1, PTPN10, VH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEX9, UniProt: P28562, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Protein Designed AR protein mbp3_16


Mass: 14787.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 85 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M DL-GLUTAMIC ACID 0.2 M DL-ALANINE 0.2 M GLYCINE 0.2 M DL-LYSINE 0.2 M DL-SERINE 0.1 M TRIS; BICINE 25% MPD 25% PEG1000 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 5, 2016
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 22649 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.1
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 2 / Num. unique obs: 2139 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MP6, 6D65

3mp6

6d65


Resolution: 2.55→38.574 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.37
RfactorNum. reflection% reflection
Rfree0.2517 1098 4.87 %
Rwork0.1819 --
obs0.1853 22558 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→38.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4877 0 47 81 5005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085063
X-RAY DIFFRACTIONf_angle_d0.9356887
X-RAY DIFFRACTIONf_dihedral_angle_d5.0823840
X-RAY DIFFRACTIONf_chiral_restr0.052763
X-RAY DIFFRACTIONf_plane_restr0.005895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5498-2.66580.31311400.23462531X-RAY DIFFRACTION96
2.6658-2.80630.32011400.22552642X-RAY DIFFRACTION100
2.8063-2.98210.29431360.2192671X-RAY DIFFRACTION100
2.9821-3.21220.32251280.21872670X-RAY DIFFRACTION100
3.2122-3.53530.26391260.19742690X-RAY DIFFRACTION100
3.5353-4.04630.24621500.16692668X-RAY DIFFRACTION100
4.0463-5.09610.22191400.15312725X-RAY DIFFRACTION100
5.0961-38.5780.22111380.17342863X-RAY DIFFRACTION100

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