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- PDB-5njk: PTB domain of human Numb isoform-1 -

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Basic information

Entry
Database: PDB / ID: 5njk
TitlePTB domain of human Numb isoform-1
Components
  • ALA-TYR-ILE-GLY-PRO-PTR-LEU
  • Protein numb homolog
KeywordsENDOCYTOSIS / PTB domain / Numb / breast cancer
Function / homology
Function and homology information


neuroblast division in subventricular zone / lateral ventricle development / alpha-catenin binding / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of protein localization to plasma membrane / adherens junction organization / clathrin-coated vesicle / positive regulation of neurogenesis / Recycling pathway of L1 / clathrin-coated pit ...neuroblast division in subventricular zone / lateral ventricle development / alpha-catenin binding / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of protein localization to plasma membrane / adherens junction organization / clathrin-coated vesicle / positive regulation of neurogenesis / Recycling pathway of L1 / clathrin-coated pit / Activated NOTCH1 Transmits Signal to the Nucleus / axonogenesis / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / beta-catenin binding / apical part of cell / cytoplasmic vesicle / basolateral plasma membrane / early endosome / endosome membrane / positive regulation of cell migration / cadherin binding / focal adhesion / glutamatergic synapse / plasma membrane / cytoplasm
Similarity search - Function
NUMB domain / Numb/numb-like / NUMB domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...NUMB domain / Numb/numb-like / NUMB domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Protein numb homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsMapelli, M. / Di Fiore, P.P.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG-18629, IG-14404, IG-18988, IG-11904 Italy
CitationJournal: J. Cell Biol. / Year: 2018
Title: A Numb-Mdm2 fuzzy complex reveals an isoform-specific involvement of Numb in breast cancer.
Authors: Colaluca, I.N. / Basile, A. / Freiburger, L. / D'Uva, V. / Disalvatore, D. / Vecchi, M. / Confalonieri, S. / Tosoni, D. / Cecatiello, V. / Malabarba, M.G. / Yang, C.J. / Kainosho, M. / ...Authors: Colaluca, I.N. / Basile, A. / Freiburger, L. / D'Uva, V. / Disalvatore, D. / Vecchi, M. / Confalonieri, S. / Tosoni, D. / Cecatiello, V. / Malabarba, M.G. / Yang, C.J. / Kainosho, M. / Sattler, M. / Mapelli, M. / Pece, S. / Di Fiore, P.P.
History
DepositionMar 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein numb homolog
B: Protein numb homolog
C: Protein numb homolog
D: Protein numb homolog
E: Protein numb homolog
F: Protein numb homolog
H: ALA-TYR-ILE-GLY-PRO-PTR-LEU
G: ALA-TYR-ILE-GLY-PRO-PTR-LEU
I: ALA-TYR-ILE-GLY-PRO-PTR-LEU
J: ALA-TYR-ILE-GLY-PRO-PTR-LEU
K: ALA-TYR-ILE-GLY-PRO-PTR-LEU
M: ALA-TYR-ILE-GLY-PRO-PTR-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,01414
Polymers112,82112
Non-polymers1922
Water362
1
A: Protein numb homolog
G: ALA-TYR-ILE-GLY-PRO-PTR-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9003
Polymers18,8042
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-14 kcal/mol
Surface area8850 Å2
MethodPISA
2
B: Protein numb homolog
K: ALA-TYR-ILE-GLY-PRO-PTR-LEU


Theoretical massNumber of molelcules
Total (without water)18,8042
Polymers18,8042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-8 kcal/mol
Surface area9180 Å2
MethodPISA
3
C: Protein numb homolog
I: ALA-TYR-ILE-GLY-PRO-PTR-LEU


Theoretical massNumber of molelcules
Total (without water)18,8042
Polymers18,8042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8 kcal/mol
Surface area8160 Å2
MethodPISA
4
D: Protein numb homolog
J: ALA-TYR-ILE-GLY-PRO-PTR-LEU


Theoretical massNumber of molelcules
Total (without water)18,8042
Polymers18,8042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-7 kcal/mol
Surface area8400 Å2
MethodPISA
5
E: Protein numb homolog
H: ALA-TYR-ILE-GLY-PRO-PTR-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9003
Polymers18,8042
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-21 kcal/mol
Surface area8260 Å2
MethodPISA
6
F: Protein numb homolog
M: ALA-TYR-ILE-GLY-PRO-PTR-LEU


Theoretical massNumber of molelcules
Total (without water)18,8042
Polymers18,8042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-7 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.270, 81.870, 235.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein numb homolog / h-Numb / Protein S171


Mass: 17927.674 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: PTB domain / Source: (gene. exp.) Homo sapiens (human) / Gene: NUMB / Production host: Escherichia coli BL21 / References: UniProt: P49757
#2: Protein/peptide
ALA-TYR-ILE-GLY-PRO-PTR-LEU


Mass: 875.902 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25 % PEG 3350, 0.2 M Lithium Sulfate, and 0.1 M Bis-Tris pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.13→40 Å / Num. obs: 26321 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 9.5
Reflection shellResolution: 3.13→3.24 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 1.6 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FOW

3fow


Resolution: 3.13→38.668 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.13
RfactorNum. reflection% reflection
Rfree0.2604 1336 5.08 %
Rwork0.2296 --
obs0.2312 26321 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.13→38.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 10 2 6984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157111
X-RAY DIFFRACTIONf_angle_d1.8579547
X-RAY DIFFRACTIONf_dihedral_angle_d15.4792609
X-RAY DIFFRACTIONf_chiral_restr0.081024
X-RAY DIFFRACTIONf_plane_restr0.0111209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13-3.24180.34011360.30692394X-RAY DIFFRACTION98
3.2418-3.37160.33361350.29992475X-RAY DIFFRACTION100
3.3716-3.52490.29211280.26892454X-RAY DIFFRACTION100
3.5249-3.71060.32461350.24942479X-RAY DIFFRACTION100
3.7106-3.94290.26621250.23142476X-RAY DIFFRACTION100
3.9429-4.2470.25671410.21992473X-RAY DIFFRACTION100
4.247-4.67370.24271560.19762475X-RAY DIFFRACTION100
4.6737-5.34850.2031330.19712516X-RAY DIFFRACTION100
5.3485-6.73280.23281190.23962564X-RAY DIFFRACTION100
6.7328-38.67130.25471280.21192679X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.5275 Å / Origin y: 31.2933 Å / Origin z: -37.7806 Å
111213212223313233
T0.4676 Å20.0389 Å2-0.0031 Å2-0.4663 Å2-0.0212 Å2--0.4551 Å2
L0.3043 °20.0317 °20.1492 °2-0.3529 °2-0.0844 °2--0.2566 °2
S-0.049 Å °-0.1246 Å °0.1151 Å °0.1293 Å °-0.0046 Å °0.039 Å °-0.0317 Å °-0.0191 Å °0.0331 Å °
Refinement TLS groupSelection details: all

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