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- PDB-5fu7: drosophila nanos NBR peptide bound to the NOT module of the human... -

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Basic information

Entry
Database: PDB / ID: 5fu7
Titledrosophila nanos NBR peptide bound to the NOT module of the human CCR4-NOT complex
Components
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
  • NANOS, ISOFORM B
KeywordsGENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / TRANSCRIPTION / TRANSLATIONAL REPRESSION
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / trophectodermal cell differentiation ...positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / peroxisomal membrane / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription corepressor binding / nuclear estrogen receptor binding / P-body / transcription coregulator activity / regulation of translation / positive regulation of cold-induced thermogenesis / negative regulation of translation / molecular adaptor activity / protein domain specific binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / extracellular space / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nanos/Xcat2 / Zinc finger, nanos-type / Nanos domain superfamily / Nanos RNA binding domain / Zinc finger nanos-type profile. / CCR4-NOT complex subunit 2/3/5, C-terminal domain / CCR4-Not complex component, Not N-terminal domain / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / NOT2/NOT3/NOT5, C-terminal ...Nanos/Xcat2 / Zinc finger, nanos-type / Nanos domain superfamily / Nanos RNA binding domain / Zinc finger nanos-type profile. / CCR4-NOT complex subunit 2/3/5, C-terminal domain / CCR4-Not complex component, Not N-terminal domain / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / NOT2/NOT3/NOT5, C-terminal / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5 / NOT2/NOT3/NOT5 C-terminal / CCR4-Not complex component, Not1, C-terminal / CCR4-NOT transcription complex subunit 1, domain 4 / CCR4-NOT transcription complex subunit 1, CAF1-binding domain / CCR4-NOT transcription complex subunit 1, TTP binding domain / CCR4-NOT transcription complex subunit 1, HEAT repeat / CCR4-NOT subunit 1, TTP binding domain superfamily / CCR4-NOT transcription complex subunit 1 / CCR4-Not complex component, Not1 / CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 / CCR4-NOT transcription complex subunit 1 CAF1-binding domain / CCR4-NOT transcription complex subunit 1 TTP binding domain / CCR4-NOT transcription complex subunit 1 HEAT repeat / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Nanos, isoform B / CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 3 / CCR4-NOT transcription complex subunit 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
DROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRaisch, T. / Bhandari, D. / Sabath, K. / Helms, S. / Valkov, E. / Weichenrieder, O. / Izaurralde, E.
CitationJournal: Embo J. / Year: 2016
Title: Distinct Modes of Recruitment of the Ccr4-not Complex by Drosophila and Vertebrate Nanos
Authors: Raisch, T. / Bhandari, D. / Sabath, K. / Helms, S. / Valkov, E. / Weichenrieder, O. / Izaurralde, E.
History
DepositionJan 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURES OF CHAINS B, C, F, G ARE ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURES OF CHAINS B, C, F, G ARE BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED EACH FOR CHAINS B, C, F, G.

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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 1
B: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
D: NANOS, ISOFORM B
E: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
F: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
G: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
H: NANOS, ISOFORM B


Theoretical massNumber of molelcules
Total (without water)217,1568
Polymers217,1568
Non-polymers00
Water0
1
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
B: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
D: NANOS, ISOFORM B


Theoretical massNumber of molelcules
Total (without water)108,5784
Polymers108,5784
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17220 Å2
ΔGint-97.3 kcal/mol
Surface area38540 Å2
MethodPISA
2
E: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
F: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
G: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
H: NANOS, ISOFORM B


Theoretical massNumber of molelcules
Total (without water)108,5784
Polymers108,5784
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16750 Å2
ΔGint-93.9 kcal/mol
Surface area37950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.950, 135.670, 104.970
Angle α, β, γ (deg.)90.00, 107.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 / CCR4-ASSOCIATED FACTOR 1 / NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 HOMOLOG / NOT1H / HNOT1


Mass: 61620.102 Da / Num. of mol.: 2
Fragment: NOT1 SUPERFAMILY HOMOLOGY DOMAIN, RESIDUES 1833- 2361
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN(PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A5YKK6
#2: Protein CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2 / CCR4-ASSOCIATED FACTOR 2


Mass: 22945.076 Da / Num. of mol.: 2
Fragment: NOT ANCHOR REGION AND NOT-BOX DOMAIN, RESIDUES 350-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN(PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9NZN8
#3: Protein CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3 / CCR4-ASSOCIATED FACTOR 3 / LEUKOCYTE RECEPTOR CLUSTER MEMBER 2


Mass: 18267.590 Da / Num. of mol.: 2
Fragment: NOT ANCHOR REGION AND NOT-BOX DOMAIN, RESIDUES 607-748
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN(PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: O75175
#4: Protein NANOS, ISOFORM B


Mass: 5745.219 Da / Num. of mol.: 2 / Fragment: NOT MODULE BINDING REGION (NBR), RESIDUES 116-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN(PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A0A0B4KGY5
Sequence detailsCHAIN A, E. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN B, F. THE SIX N- ...CHAIN A, E. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN B, F. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN C, G. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN D, H. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG.

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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: 2.5 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growpH: 6 / Details: 0.1 M MES PH 6.0, 260 MM LICL, 18.6 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2015 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 36658 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.45 % / Biso Wilson estimate: 95.64 Å2 / Rsym value: 0.08 / Net I/σ(I): 13
Reflection shellResolution: 3.1→3.17 Å / Redundancy: 3.45 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.74 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C0D

4c0d


Resolution: 3.1→48.58 Å / Cor.coef. Fo:Fc: 0.9428 / Cor.coef. Fo:Fc free: 0.9065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.422
Details: THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, 1833 TO 1838, 2004 TO 2007. CHAIN B, 540. CHAIN D, 116 TO 119, 135 TO 143, 162, 163. CHAIN E, 1833 TO 1840, 2004 TO 2010 CHAIN F, 540. CHAIN ...Details: THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, 1833 TO 1838, 2004 TO 2007. CHAIN B, 540. CHAIN D, 116 TO 119, 135 TO 143, 162, 163. CHAIN E, 1833 TO 1840, 2004 TO 2010 CHAIN F, 540. CHAIN H, 116 TO 119, 132 TO 142, 161 TO 163. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUE 2361. CHAIN D, RESIDUES 125, 132, 146, 150. CHAIN E, RESIDUE 2361. CHAIN H, RESIDUES 122, 125, 128, 145, 146, 150, 157, 160.
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1892 5.16 %RANDOM
Rwork0.1649 ---
obs0.168 36657 99.68 %-
Displacement parametersBiso mean: 99.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.321 Å20 Å20.1262 Å2
2--23.036 Å20 Å2
3----23.357 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: LAST / Resolution: 3.1→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14548 0 0 0 14548
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114959HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.120320HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5091SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes365HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2145HARMONIC5
X-RAY DIFFRACTIONt_it14959HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion21.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1913SEMIHARMONIC5
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_contact17702SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.19 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2512 163 5.54 %
Rwork0.2288 2781 -
all0.2301 2944 -
obs--98.2 %
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)
11.6611.379-0.45023.7465-0.99870.80330.1396-0.18580.01180.1722-0.09730.1741-0.1038-0.0194-0.0423-0.10430.04520.0709-0.2173-0.046-0.214111.7119-11.664641.2284
24.7141-0.2251-1.3180.32530.88560.23370.1451.2263-0.4556-0.4906-0.38260.2369-0.3144-0.3420.2376-0.08850.2046-0.1992-0.1723-0.121-0.00482.9093-16.478825.9711
32.4605-1.1418-1.27281.11961.29941.42490.02410.3684-0.709-0.0586-0.50470.6915-0.0114-0.45340.4806-0.23390.05010.01-0.3255-0.05370.31176.7034-21.740343.7784
41.6518-0.6047-0.25811.08350.79960.55340.0207-0.0587-0.08740.4733-0.17470.65040.04380.14970.1540.0092-0.10320.2462-0.19350.07820.114676.0635-33.202862.517
51.1788-0.24350.54983.3033-1.42251.6132-0.05710.1898-0.0392-0.4002-0.0261-0.17570.25810.18260.08320.0720.0350.0469-0.3075-0.0711-0.315187.9119-50.9116115.125
61.1328-0.27721.06840.22-0.11892.2459-0.0859-0.37220.00860.4508-0.07590.2991-0.0424-0.63090.1618-0.0004-0.01440.1407-0.2558-0.08020.079255.6208-45.8492110.2202
70.7799-0.08810.53340.510.64932.2802-0.0710.05730.0383-0.1448-0.13820.1805-0.2389-0.43250.20920.0463-0.0029-0.1066-0.214-0.00110.017361.0457-40.652392.0355
80.3888-0.21031.041900.15891.73460.0149-0.08410.0433-0.3915-0.01980.1209-0.07170.32230.00490.2937-0.03880.0746-0.12570.0444-0.141871.6542-28.688976.5157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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