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- PDB-1oig: The solution structure of the DPY module from the Dumpy protein -

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Basic information

Entry
Database: PDB / ID: 1oig
TitleThe solution structure of the DPY module from the Dumpy protein
ComponentsDumpy, isoform Y
KeywordsSTRUCTURAL PROTEIN / DROSOPHILA / DUMPY
Function / homology
Function and homology information


chitin-based cuticle attachment to epithelium / regulation of imaginal disc-derived wing size / apposition of dorsal and ventral imaginal disc-derived wing surfaces / chitin-based embryonic cuticle biosynthetic process / open tracheal system development / extracellular matrix structural constituent / extracellular matrix / cell projection / membrane => GO:0016020 / DNA-binding transcription factor activity ...chitin-based cuticle attachment to epithelium / regulation of imaginal disc-derived wing size / apposition of dorsal and ventral imaginal disc-derived wing surfaces / chitin-based embryonic cuticle biosynthetic process / open tracheal system development / extracellular matrix structural constituent / extracellular matrix / cell projection / membrane => GO:0016020 / DNA-binding transcription factor activity / calcium ion binding / zinc ion binding / nucleus
Similarity search - Function
Cysteine-rich repeat / Worm-specific repeat type 1 / Zinc finger, NF-X1-type / ZnF_NFX / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Calcium-binding EGF domain ...Cysteine-rich repeat / Worm-specific repeat type 1 / Zinc finger, NF-X1-type / ZnF_NFX / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Dumpy, isoform Q / Dumpy, isoform Y
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsWilkin, M.B. / Becker, M.N. / Mulvey, D. / Phan, I. / Chao, A. / Cooper, K. / Chung, H.J. / Campbell, I.D. / Baron, M. / MacIntyre, R.
CitationJournal: Curr.Biol. / Year: 2000
Title: Drosophila Dumpy is a Gigantic Extracellular Protein Required to Maintain Tension at Epidermal-Cuticle Attachment Sites
Authors: Wilkin, M.B. / Becker, M.N. / Mulvey, D. / Phan, I. / Chao, A. / Cooper, K. / Chung, H.J. / Campbell, I.D. / Baron, M. / MacIntyre, R.
History
DepositionJun 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity / entity_name_com / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation_author.name / _entity.pdbx_description / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dumpy, isoform Y


Theoretical massNumber of molelcules
Total (without water)2,6801
Polymers2,6801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 50LEAST RESTRAINT VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein/peptide Dumpy, isoform Y


Mass: 2680.006 Da / Num. of mol.: 1 / Fragment: DPY MODULE, RESIDUES 14185-14208 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: M9PC48, UniProt: M9PB30*PLUS
Compound detailsDROSOPHILA DUMPY IS A GIGANTIC EXTRACELLULAR PROTEIN REQUIRED TO MAINTAIN TENSION AT EPIDERMAL- ...DROSOPHILA DUMPY IS A GIGANTIC EXTRACELLULAR PROTEIN REQUIRED TO MAINTAIN TENSION AT EPIDERMAL-CUTICLE ATTACHMENT SITES

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR SPECTROSCOPY.

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Sample preparation

Sample conditionspH: 3.3 / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
Field strength (MHz)Spectrometer-ID
5001
6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
XPLOR3.851structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS / Conformers calculated total number: 50 / Conformers submitted total number: 22

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