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- PDB-2fnj: Crystal structure of a B30.2/SPRY domain-containing protein GUSTA... -

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Basic information

Entry
Database: PDB / ID: 2fnj
TitleCrystal structure of a B30.2/SPRY domain-containing protein GUSTAVUS in complex with Elongin B and Elongin C
Components
  • CG2944-PF, isoform F
  • Transcription elongation factor B polypeptide 1
  • Transcription elongation factor B polypeptide 2
KeywordsPROTEIN TRANSPORT/SIGNALING PROTEIN / Beta-sandwich / Lectin-like / B30.2 / SPRY / PROTEIN TRANSPORT-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / cuticle pattern formation / RNA Polymerase II Pre-transcription Events / : / Neddylation / oocyte anterior/posterior axis specification / pole plasm / Antigen processing: Ubiquitination & Proteasome degradation ...TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / cuticle pattern formation / RNA Polymerase II Pre-transcription Events / : / Neddylation / oocyte anterior/posterior axis specification / pole plasm / Antigen processing: Ubiquitination & Proteasome degradation / wing disc morphogenesis / pole plasm assembly / dorsal appendage formation / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / germ cell development / transcription corepressor binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / protein localization / positive regulation of protein catabolic process / protein-macromolecule adaptor activity / cell cortex / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription regulator complex / transcription coactivator activity / protein ubiquitination / intracellular signal transduction / ubiquitin protein ligase binding / protein-containing complex binding / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like ...SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein gustavus / Elongin-B / Elongin-C / :
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWoo, J.S. / Oh, B.H.
CitationJournal: Embo J. / Year: 2006
Title: Structural and functional insights into the B30.2/SPRY domain
Authors: Woo, J.S. / Imm, J.H. / Min, C.K. / Kim, K.J. / Cha, S.S. / Oh, B.H.
History
DepositionJan 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG2944-PF, isoform F
B: Transcription elongation factor B polypeptide 2
C: Transcription elongation factor B polypeptide 1


Theoretical massNumber of molelcules
Total (without water)49,7253
Polymers49,7253
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-26 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.308, 82.489, 118.966
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 CG2944-PF, isoform F / GUSTAVUS


Mass: 25695.596 Da / Num. of mol.: 1 / Fragment: residues 28-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7KRQ1, UniProt: A1Z6E0*PLUS
#2: Protein Transcription elongation factor B polypeptide 2 / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Elongin B / EloB / Elongin 18 kDa subunit


Mass: 13185.833 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P62869
#3: Protein Transcription elongation factor B polypeptide 1 / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Elongin C / EloC / Elongin 15 ...RNA polymerase II transcription factor SIII subunit C / SIII p15 / Elongin C / EloC / Elongin 15 kDa subunit / Stromal membrane-associated protein SMAP1B homolog


Mass: 10843.420 Da / Num. of mol.: 1 / Fragment: residues 17-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P83940
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.2M di-Ammonium Tartrate, 20% w/v Polyethylene Glycol 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11281
21281
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11.0064
SYNCHROTRONPAL/PLS 6B20.97903
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 7, 2005
ADSC QUANTUM 42CCDApr 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00641
20.979031
ReflectionRedundancy: 5.8 % / Av σ(I) over netI: 16 / Number: 153863 / Rmerge(I) obs: 0.085 / Χ2: 1.72 / D res high: 2.7 Å / D res low: 30 Å / Num. obs: 26477 / % possible obs: 99
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
5.830268399.60.0421.5116.8
4.615.8267599.80.0631.8166.8
4.034.6126661000.0682.1256.8
3.664.03258897.50.0832.3186.3
3.43.66259396.50.0982.185.7
3.23.4265699.40.1131.6946
3.043.2265699.60.1371.4025.6
2.913.04265799.50.1681.2855.1
2.82.91267799.40.2031.1594.7
2.72.8262698.80.2461.2434.3
ReflectionResolution: 1.8→30 Å / Num. all: 46868 / Num. obs: 44051 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.069 / Χ2: 1.774 / Net I/σ(I): 16
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 80.9 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.351 / Num. unique obs: 3736 / Χ2: 0.449 / % possible all: 94

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Phasing

Phasing dmFOM : 0.73 / FOM acentric: 0.74 / FOM centric: 0.66 / Reflection: 12774 / Reflection acentric: 10910 / Reflection centric: 1864
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-29.4890.860.890.8618397221
5-80.840.870.717761406370
4-50.870.890.7321771838339
3.5-40.820.840.7520881815273
3-3.50.680.690.5937793357422
2.8-30.490.490.4223362097239

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.08phasing
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / FOM work R set: 0.824 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2472 2193 4.7 %
Rwork0.2183 --
all0.351 46868 -
obs-43922 94.2 %
Solvent computationBsol: 41.108 Å2
Displacement parametersBiso mean: 31.402 Å2
Baniso -1Baniso -2Baniso -3
1--2.271 Å20 Å20 Å2
2--4.298 Å20 Å2
3----2.027 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 0 298 3508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.3121
X-RAY DIFFRACTIONc_bond_d0.0052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 43

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.8-1.810.377440.389777821
1.81-1.830.322360.382795831
1.83-1.840.358410.359858899
1.84-1.860.288360.34875911
1.86-1.880.334330.343878911
1.88-1.890.332400.326879919
1.89-1.910.332540.335882936
1.91-1.930.308440.32933977
1.93-1.950.349420.313912954
1.95-1.970.323440.304918962
1.97-1.990.324580.313914972
1.99-2.010.32600.2929641024
2.01-2.030.28670.272917984
2.03-2.050.284630.272923986
2.05-2.080.293460.27944990
2.08-2.10.305520.2469951047
2.1-2.130.234500.243944994
2.13-2.160.345530.239944997
2.16-2.190.333590.2559701029
2.19-2.220.278520.237941993
2.22-2.250.249490.22410081057
2.25-2.290.261370.22110081045
2.29-2.320.249380.2239941032
2.32-2.360.277540.2279951049
2.36-2.410.245450.229921037
2.41-2.450.259520.2129721024
2.45-2.50.235550.20910061061
2.5-2.560.207420.20610131055
2.56-2.620.294520.2079861038
2.62-2.680.277540.2310141068
2.68-2.750.259470.23310251072
2.75-2.830.293550.22110111066
2.83-2.920.238630.2229931056
2.92-3.030.297560.23110271083
3.03-3.150.263600.21510431103
3.15-3.290.247620.20910041066
3.29-3.470.239660.21310241090
3.47-3.680.218540.20210491103
3.68-3.960.237480.18610551103
3.96-4.360.17480.15910731121
4.36-4.980.189660.15510611127
4.98-6.240.236480.210901138
6.24-200.188680.17811231191
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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