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- PDB-9fu8: Structure of the ASH1 domain of Drosophila melanogaster Spd-2 -

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Basic information

Entry
Database: PDB / ID: 9fu8
TitleStructure of the ASH1 domain of Drosophila melanogaster Spd-2
ComponentsBcDNA.LD24702
KeywordsCYTOSOLIC PROTEIN / Centrosome / pericentriolar material / Drosophila
Function / homology
Function and homology information


sperm aster formation / apyrase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / astral microtubule organization / centrosome cycle / pericentriolar material / centriole / centrosome
Similarity search - Function
ADP-ribose pyrophosphatase, mitochondrial / : / : / : / Cep192 domain 4 / Cep192 domain 5 / Cep192 domain 6
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsSheppard, D. / Feng, Z. / Lea, S.M. / Johnson, S. / Raff, J.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust215523 United Kingdom
Wellcome Trust209194 United Kingdom
CitationJournal: Sci Adv / Year: 2025
Title: The conserved Spd-2/CEP192 domain adopts a unique protein fold to promote centrosome scaffold assembly.
Authors: Hu, L. / Wainman, A. / Andreeva, A. / Apizi, M. / Alvarez-Rodrigo, I. / Wong, S.S. / Saurya, S. / Sheppard, D. / Cottee, M. / Johnson, S. / Lea, S.M. / Raff, J.W. / van Breugel, M. / Feng, Z.
History
DepositionJun 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BcDNA.LD24702


Theoretical massNumber of molelcules
Total (without water)11,9611
Polymers11,9611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein BcDNA.LD24702 / Spindle defective 2


Mass: 11960.872 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: spd-2, anon-73Ba, BcDNA.LD24702, BcDNA:LD24702, CEP192, Cep192, CG17286-PA, D-SPD2, D-Spd2, Dmel\CG17286, DSPD-2, DSpd-2, Dspd-2, DSpd2, Dspd2, dSpd2, SPD-2, Spd-2, SPD2, Spd2, spd2, CG17286, Dmel_CG17286
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VV79, ADP-ribose diphosphatase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic13D CBCA(CO)NH
141isotropic13D CBCANH
151isotropic13D HNCO
191isotropic13D HNHA
181isotropic13D (H)CCH-TOCSY
171isotropic13D (H)CC(CO)NH
161isotropic13D CC(CO)NH
1101isotropic23D 1H-13C NOESY aliphatic
1111isotropic23D 1H-13C NOESY aromatic
1121isotropic23D 1H-15N NOESY
1131isotropic23D 1H-13C-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 100 mM Na2HPO4, 137 mM NaCl, 27 mM KCl, 18 mM KH2PO4, 1 uM ZnCl2, 1 mM DTT, 0.5 mM [U-13C; U-15N] Spd-2, 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMNa2HPO4natural abundance1
137 mMNaClnatural abundance1
27 mMKClnatural abundance1
18 mMKH2PO4natural abundance1
1 uMZnCl2natural abundance1
1 mMDTTnatural abundance1
0.5 mMSpd-2[U-13C; U-15N]1
Sample conditionsIonic strength: 0.196 Not defined / Label: 13C_15N_sample / pH: 7 / Pressure: 1 atm / Temperature: 20 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II5001
Bruker AVANCE IIBrukerAVANCE II6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYShin J, Lee W, Lee W.peak picking
NMRFAM-SPARKYShin J, Lee W, Lee W.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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