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- PDB-5onb: Drosophila Bag-of-marbles CBM peptide bound to human CAF40 -

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Basic information

Entry
Database: PDB / ID: 5onb
TitleDrosophila Bag-of-marbles CBM peptide bound to human CAF40
Components
  • CCR4-NOT transcription complex subunit 9
  • Protein bag-of-marbles
KeywordsGENE REGULATION / DEADENYLATION / CCR4-NOT / TRANSLATIONAL REPRESSION / TRANSLATION
Function / homology
Function and homology information


male germline stem cell symmetric division / cystoblast division / spectrosome / fusome organization / germarium-derived female germ-line cyst formation / negative regulation of peptidoglycan recognition protein signaling pathway / fusome / germ-line stem cell division / positive regulation of protein deubiquitination / cell competition in a multicellular organism ...male germline stem cell symmetric division / cystoblast division / spectrosome / fusome organization / germarium-derived female germ-line cyst formation / negative regulation of peptidoglycan recognition protein signaling pathway / fusome / germ-line stem cell division / positive regulation of protein deubiquitination / cell competition in a multicellular organism / CCR4-NOT core complex / female germ-line stem cell asymmetric division / CCR4-NOT complex / spermatogonial cell division / nuclear-transcribed mRNA poly(A) tail shortening / germ-line stem cell population maintenance / sex differentiation / gamete generation / positive regulation of stem cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / positive regulation of protein K63-linked deubiquitination / positive regulation of smoothened signaling pathway / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / epidermal growth factor receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / oogenesis / positive regulation of peptidyl-serine phosphorylation / mRNA regulatory element binding translation repressor activity / ubiquitin binding / mRNA 3'-UTR binding / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / spermatogenesis / transcription coactivator activity / negative regulation of translation / protein domain specific binding / protein homodimerization activity / protein-containing complex / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Protein bag of marbles / CCR4-NOT transcription complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRaisch, T. / Sgromo, A. / Backhaus, C. / Izaurralde, E. / Weichenrieder, O.
CitationJournal: RNA / Year: 2018
Title: DrosophilaBag-of-marbles directly interacts with the CAF40 subunit of the CCR4-NOT complex to elicit repression of mRNA targets.
Authors: Sgromo, A. / Raisch, T. / Backhaus, C. / Keskeny, C. / Alva, V. / Weichenrieder, O. / Izaurralde, E.
History
DepositionAug 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCR4-NOT transcription complex subunit 9
B: Protein bag-of-marbles
C: CCR4-NOT transcription complex subunit 9
D: Protein bag-of-marbles
E: CCR4-NOT transcription complex subunit 9
F: Protein bag-of-marbles
G: CCR4-NOT transcription complex subunit 9
H: Protein bag-of-marbles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,8779
Polymers135,7858
Non-polymers921
Water00
1
A: CCR4-NOT transcription complex subunit 9
B: Protein bag-of-marbles


Theoretical massNumber of molelcules
Total (without water)33,9462
Polymers33,9462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-10 kcal/mol
Surface area13570 Å2
MethodPISA
2
C: CCR4-NOT transcription complex subunit 9
D: Protein bag-of-marbles


Theoretical massNumber of molelcules
Total (without water)33,9462
Polymers33,9462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-13 kcal/mol
Surface area13510 Å2
MethodPISA
3
E: CCR4-NOT transcription complex subunit 9
F: Protein bag-of-marbles


Theoretical massNumber of molelcules
Total (without water)33,9462
Polymers33,9462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-11 kcal/mol
Surface area13980 Å2
MethodPISA
4
G: CCR4-NOT transcription complex subunit 9
H: Protein bag-of-marbles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0383
Polymers33,9462
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-11 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.570, 200.930, 59.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
CCR4-NOT transcription complex subunit 9 / Cell differentiation protein RQCD1 homolog / Rcd-1


Mass: 31072.189 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The first six residues (GPHMLE) remain from the protease cleavage site and the linker.
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT9, RCD1, RQCD1 / Plasmid: PETMCN (PNEA) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q92600
#2: Protein/peptide
Protein bag-of-marbles


Mass: 2874.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P22745
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES (pH 7.0) 200 mM CaCl2 15% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0396 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2015 / Details: focussing mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0396 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 26082 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 90.68 Å2 / Rsym value: 0.095 / Net I/σ(I): 13.2
Reflection shellResolution: 3→3.08 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1852 / Rsym value: 1.008 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FV2

2fv2


Resolution: 3→46.73 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.8941 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.471
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 1263 4.84 %RANDOM
Rwork0.2156 ---
obs0.2182 26082 99.57 %-
Displacement parametersBiso mean: 100.72 Å2
Baniso -1Baniso -2Baniso -3
1--15.9572 Å20 Å20 Å2
2--13.3529 Å20 Å2
3---2.6043 Å2
Refine analyzeLuzzati coordinate error obs: 0.448 Å
Refinement stepCycle: 1 / Resolution: 3→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 6 0 9358
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019533HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0812932HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3405SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes245HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1337HARMONIC5
X-RAY DIFFRACTIONt_it9533HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion19.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1282SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11506SEMIHARMONIC4
LS refinement shellResolution: 3→3.12 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3407 136 4.73 %
Rwork0.2601 2739 -
all0.264 2875 -
obs--99.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.171-0.56440.22195.25950.03793.11070.01220.29250.2651-0.80.19890.3983-0.33220.1642-0.2111-0.0118-0.0814-0.1641-0.19120.0038-0.1635-19.14715.3837-41.1186
22.32255.0796-3.14522.86490.981111.37920.02250.36980.0836-0.13740.11530.0337-0.02250.3228-0.13780.3076-0.0985-0.17950.0185-0.1647-0.3592-14.82736.1632-51.2463
35.73091.87692.12698.9342-0.60783.8270.3987-0.6223-0.631-0.11650.14240.09060.499-0.4087-0.5412-0.1196-0.0712-0.1143-0.08230.0884-0.4762-22.406-8.0871-14.1046
42.3596-1.84433.33882.64190.315413.2162-0.03420.02340.0997-0.0512-0.0957-0.1818-0.196-0.21580.12990.6079-0.0045-0.1414-0.0101-0.0939-0.5973-15.895-2.1373-2.3941
56.06944.6406-0.87697.1018-2.05013.0067-0.46460.66570.1689-0.25050.59650.23920.2143-0.8507-0.1319-0.3198-0.012-0.0368-0.0635-0.1066-0.2828-39.491544.1987-18.6714
66.6501-4.3812-1.93430.5483-4.97533.44160.025-0.08050.2093-0.12680.12010.18620.112-0.2306-0.1451-0.30350.20740.14860.07120.09220.1677-48.766353.9313-14.6501
72.91942.4866-0.33816.9738-0.17394.5850.18270.0424-0.33110.07060.1679-0.6654-0.13460.1281-0.3506-0.29490.0478-0.0758-0.16640.0445-0.1225-8.063162.5039-16.9065
86.7531-0.36772.48151.01171.11590.84850.1419-0.1616-0.164-0.0323-0.0867-0.2630.0887-0.0398-0.0552-0.11640.1063-0.2685-0.13320.07620.28890.90453.3584-9.4159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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