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- PDB-2nmb: DNUMB PTB DOMAIN COMPLEXED WITH A PHOSPHOTYROSINE PEPTIDE, NMR, E... -

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Basic information

Entry
Database: PDB / ID: 2nmb
TitleDNUMB PTB DOMAIN COMPLEXED WITH A PHOSPHOTYROSINE PEPTIDE, NMR, ENSEMBLE OF STRUCTURES.
Components
  • PROTEIN (GPPY PEPTIDE)
  • PROTEIN (NUMB PROTEIN)
KeywordsCELL CYCLE/GENE REGULATION / COMPLEX / SIGNAL TRANSDUCTION / PHOSPHOTYROSINE BINDING DOMAIN (PTB) / ASYMETR IC CELL DIVISION / CELL CYCLE-GENE REGULATION COMPLEX
Function / homology
Function and homology information


pericardial nephrocyte differentiation / Malpighian tubule tip cell differentiation / enteroendocrine cell differentiation / regulation of nervous system development / sensory organ precursor cell fate determination / sensory organ precursor cell division / neuroblast development / muscle cell fate specification / regulation of asymmetric cell division / regulation of neuroblast proliferation ...pericardial nephrocyte differentiation / Malpighian tubule tip cell differentiation / enteroendocrine cell differentiation / regulation of nervous system development / sensory organ precursor cell fate determination / sensory organ precursor cell division / neuroblast development / muscle cell fate specification / regulation of asymmetric cell division / regulation of neuroblast proliferation / glial cell migration / asymmetric neuroblast division / negative regulation of receptor recycling / basal part of cell / embryonic heart tube development / Notch binding / centrosome localization / negative regulation of neuroblast proliferation / positive regulation of endocytosis / negative regulation of Notch signaling pathway / neuroblast proliferation / regulation of neurogenesis / intracellular protein localization / cell cortex / negative regulation of gene expression / ATP binding / nucleus / 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
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / SIMULATED ANNEALING WITH AMBIGUOUS RESTRAINTS
AuthorsLi, S.-C. / Zwahlen, C. / Vincent, S.J.F. / McGlade, C.J. / Pawson, T. / Forman-Kay, J.D.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of a Numb PTB domain-peptide complex suggests a basis for diverse binding specificity.
Authors: Li, S.C. / Zwahlen, C. / Vincent, S.J. / McGlade, C.J. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: High-Affinity Binding of the Drosophila Numb Phosphotyrosine-Binding Domain to Pep Tides Containing a Gly-Pro-(P)Tyr Motif
Authors: Li, S.-C. / Songyang, Z. / Vincent, S.J.F. / Zwahlen, C. / Wiley, S. / Cantley, L. / Kay, L.E. / Forman-Kay, J.D. / Pawson, T.
History
DepositionOct 29, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 16, 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: PROTEIN (NUMB PROTEIN)
B: PROTEIN (GPPY PEPTIDE)


Theoretical massNumber of molelcules
Total (without water)18,7902
Polymers18,7902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 200NO NOE VIOLATION > 0.3 A
RepresentativeModel #4

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Components

#1: Protein PROTEIN (NUMB PROTEIN)


Mass: 17914.402 Da / Num. of mol.: 1 / Fragment: PTB DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: NUMB / Plasmid: PGEX4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P16554
#2: Protein/peptide PROTEIN (GPPY PEPTIDE)


Mass: 875.902 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121CBCACONNH
131HAHBCBCACONNH
141CCCTOCSYCONNH
151HCCTOCSYCONNH
161HCCHTOCSY
171N-NOESY HSQC
181CN-NOESY
191C-HSQC-NOESY
1101VAL-CB-NOESY
1111HALF-FILTER-NOESY
1121FILTER-NOESY
1131FILTER-TOCSY
NMR detailsText: NOE MIXING TIME 50MS AND 90MS FOR N-NOESY-HSQC, C-HSQC-NOESY, CN-NOESY NOE MIXING TIME 150MS FOR HALF-FILTER-NOESY,FILTER-NOESY

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Sample preparation

Sample conditionspH: 6 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
ARIA/X-PLOR3.851structure solution
RefinementMethod: SIMULATED ANNEALING WITH AMBIGUOUS RESTRAINTS / Software ordinal: 1
Details: MODIFICATION OF X-PLOR TO INCORPORATE ARIA PROTOCOL FOR AMBIGUOUS NOE ASSIGNMENT.
NMR ensembleConformer selection criteria: NO NOE VIOLATION > 0.3 A / Conformers calculated total number: 200 / Conformers submitted total number: 14

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