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- PDB-5crv: Crystal structure of the Bro domain of HD-PTP in a complex with t... -

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Basic information

Entry
Database: PDB / ID: 5crv
TitleCrystal structure of the Bro domain of HD-PTP in a complex with the core region of STAM2
Components
  • Signal transducing adapter molecule 2
  • Tyrosine-protein phosphatase non-receptor type 23
KeywordsPROTEIN TRANSPORT / HD-PTP / Bro domain / STAM2 / ESCRT-0 / EGFR
Function / homology
Function and homology information


positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / ESCRT-0 complex / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / ESCRT-0 complex / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / endocytic recycling / Interleukin-37 signaling / RHOU GTPase cycle / cilium assembly / endocytic vesicle / dephosphorylation / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol binding / protein-tyrosine-phosphatase / InlB-mediated entry of Listeria monocytogenes into host cell / ciliary basal body / ubiquitin binding / protein tyrosine phosphatase activity / macroautophagy / EGFR downregulation / Negative regulation of MET activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / early endosome / nuclear body / Ub-specific processing proteases / endosome / intracellular membrane-bounded organelle / protein kinase binding / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / STAM2, SH3 domain / alix/aip1 like domains / Vacuolar protein-sorting protein Bro1-like / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. ...: / STAM2, SH3 domain / alix/aip1 like domains / Vacuolar protein-sorting protein Bro1-like / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Ubiquitin interaction motif / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / SH3 domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Signal transducing adapter molecule 2 / Tyrosine-protein phosphatase non-receptor type 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsLee, J. / Ku, B. / Kim, S.J.
CitationJournal: Plos One / Year: 2016
Title: Structural Study of the HD-PTP Bro1 Domain in a Complex with the Core Region of STAM2, a Subunit of ESCRT-0
Authors: Lee, J. / Oh, K.-J. / Lee, D. / Kim, B.Y. / Choi, J.S. / Ku, B. / Kim, S.J.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 23
B: Tyrosine-protein phosphatase non-receptor type 23
C: Signal transducing adapter molecule 2
D: Signal transducing adapter molecule 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0035
Polymers85,9114
Non-polymers921
Water6,575365
1
A: Tyrosine-protein phosphatase non-receptor type 23
C: Signal transducing adapter molecule 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0483
Polymers42,9562
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-10 kcal/mol
Surface area17700 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 23
D: Signal transducing adapter molecule 2


Theoretical massNumber of molelcules
Total (without water)42,9562
Polymers42,9562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-11 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.647, 37.218, 140.019
Angle α, β, γ (deg.)90.00, 103.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 23 / His domain-containing protein tyrosine phosphatase / HD-PTP / Protein tyrosine phosphatase TD14 / PTP-TD14


Mass: 40584.816 Da / Num. of mol.: 2 / Fragment: UNP residues 1-361 / Mutation: N33A,Y34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN23, KIAA1471 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3S7, protein-tyrosine-phosphatase
#2: Protein/peptide Signal transducing adapter molecule 2 / STAM-2 / Hrs-binding protein


Mass: 2370.781 Da / Num. of mol.: 2 / Fragment: UNP residues 350-370 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75886
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris, 30%(w/v) polyethylene glycol 3350, 4%(v/v) acetonitrile

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 56289 / % possible obs: 97.3 % / Redundancy: 4.8 % / Net I/σ(I): 30.4
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 4.6 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RAU

3rau


Resolution: 2.001→29.089 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 23.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 2020 3.69 %
Rwork0.2125 --
obs0.2137 54756 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→29.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5956 0 6 365 6327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036082
X-RAY DIFFRACTIONf_angle_d0.7018211
X-RAY DIFFRACTIONf_dihedral_angle_d15.7692297
X-RAY DIFFRACTIONf_chiral_restr0.05905
X-RAY DIFFRACTIONf_plane_restr0.0031061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0012-2.05120.30451520.2733684X-RAY DIFFRACTION95
2.0512-2.10670.27311330.25853664X-RAY DIFFRACTION97
2.1067-2.16860.25871330.2443740X-RAY DIFFRACTION97
2.1686-2.23860.2841460.24213560X-RAY DIFFRACTION93
2.2386-2.31860.3051330.26693541X-RAY DIFFRACTION92
2.3186-2.41140.2621440.23183714X-RAY DIFFRACTION97
2.4114-2.52110.2661410.22663775X-RAY DIFFRACTION98
2.5211-2.65390.2941470.22193846X-RAY DIFFRACTION99
2.6539-2.82010.26621420.2253784X-RAY DIFFRACTION99
2.8201-3.03760.24141520.22823802X-RAY DIFFRACTION99
3.0376-3.34290.25781410.22073853X-RAY DIFFRACTION99
3.3429-3.82570.21091470.19943832X-RAY DIFFRACTION98
3.8257-4.81640.20251500.17053909X-RAY DIFFRACTION99
4.8164-29.09170.19791590.18114032X-RAY DIFFRACTION99

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