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- PDB-2ihs: Crystal structure of the B30.2/SPRY domain of GUSTAVUS in complex... -

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Basic information

Entry
Database: PDB / ID: 2ihs
TitleCrystal structure of the B30.2/SPRY domain of GUSTAVUS in complex with a 20-residue VASA peptide
Components
  • 20-mer from ATP-dependent RNA helicase vasa
  • CG2944-PF, isoform F
KeywordsPEPTIDE BINDING PROTEIN / B30.2/SPRY / GUSTAVUS / VASA / SPRY-containing SOCS box / F-box-SPRY / TRIM family
Function / homology
Function and homology information


cuticle pattern formation / oocyte anterior/posterior axis specification / Neddylation / pole plasm / posterior cell cortex / wing disc morphogenesis / Antigen processing: Ubiquitination & Proteasome degradation / pole plasm assembly / dorsal appendage formation / secondary piRNA processing ...cuticle pattern formation / oocyte anterior/posterior axis specification / Neddylation / pole plasm / posterior cell cortex / wing disc morphogenesis / Antigen processing: Ubiquitination & Proteasome degradation / pole plasm assembly / dorsal appendage formation / secondary piRNA processing / gamete generation / germ cell migration / elongin complex / P granule / germ cell nucleus / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / oogenesis / germ cell development / positive regulation of protein catabolic process / intracellular protein localization / cell cortex / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / RNA helicase activity / intracellular signal transduction / RNA helicase / mRNA binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Ded1/Dbp1, DEAD-box helicase domain / : / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif ...Ded1/Dbp1, DEAD-box helicase domain / : / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Concanavalin A-like lectin/glucanase domain superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein gustavus / ATP-dependent RNA helicase vasa / :
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsWoo, J.S. / Park, S.Y. / Oh, B.H.
CitationJournal: Mol.Cell / Year: 2006
Title: Structural Basis for Protein Recognition by B30.2/SPRY Domains
Authors: Woo, J.S. / Suh, H.Y. / Park, S.Y. / Oh, B.H.
History
DepositionSep 27, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 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: CG2944-PF, isoform F
B: CG2944-PF, isoform F
C: 20-mer from ATP-dependent RNA helicase vasa
D: 20-mer from ATP-dependent RNA helicase vasa


Theoretical massNumber of molelcules
Total (without water)53,3574
Polymers53,3574
Non-polymers00
Water2,558142
1
A: CG2944-PF, isoform F
C: 20-mer from ATP-dependent RNA helicase vasa


Theoretical massNumber of molelcules
Total (without water)26,6782
Polymers26,6782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-3 kcal/mol
Surface area10800 Å2
MethodPISA
2
B: CG2944-PF, isoform F
D: 20-mer from ATP-dependent RNA helicase vasa


Theoretical massNumber of molelcules
Total (without water)26,6782
Polymers26,6782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-5 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.209, 80.209, 159.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CG2944-PF, isoform F / GUSTAVUS/CG2944


Mass: 24180.625 Da / Num. of mol.: 2 / Fragment: B30.2/SPRY domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: gus / Plasmid: pPROEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIG / References: UniProt: Q7KRQ1, UniProt: A1Z6E0*PLUS
#2: Protein/peptide 20-mer from ATP-dependent RNA helicase vasa / Antigen Mab46F11


Mass: 2497.696 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: gus / Plasmid: pPROEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIG
References: UniProt: P09052, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% (w/v) PEG 8000, 0.2M calcium acetate, 0.1M imidazole (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 27426 / Num. obs: 26376 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.036 / Net I/σ(I): 37.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2143 / Rsym value: 0.224 / % possible all: 79.9

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementStarting model: PDP ENTRY 2FNJ

2fnj


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1271 -random
Rwork0.219 ---
all-27237 --
obs-26272 96.5 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 0 142 3600
LS refinement shellResolution: 2.2→2.23 Å
RfactorNum. reflection
Rfree0.311 28
Rwork0.2953 -
obs-719

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