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- PDB-4b8b: N-Terminal domain of the yeast Not1 -

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Basic information

Entry
Database: PDB / ID: 4b8b
TitleN-Terminal domain of the yeast Not1
ComponentsGENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


negative regulation of cytoplasmic mRNA processing body assembly / response to pheromone triggering conjugation with cellular fusion / pseudohyphal growth / CCR4-NOT core complex / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ATPase activator activity / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / P-body ...negative regulation of cytoplasmic mRNA processing body assembly / response to pheromone triggering conjugation with cellular fusion / pseudohyphal growth / CCR4-NOT core complex / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ATPase activator activity / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / P-body / molecular adaptor activity / negative regulation of translation / regulation of cell cycle / regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
CCR4-NOT transcription complex subunit 1, HEAT repeat 1 / CCR4-NOT transcription complex subunit 1 HEAT repeat / 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 transcription complex subunit 1, HEAT repeat 1 / CCR4-NOT transcription complex subunit 1 HEAT repeat / 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
Similarity search - Domain/homology
: / General negative regulator of transcription subunit 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.801 Å
AuthorsBasquin, J. / Conti, E.
CitationJournal: Mol.Cell / Year: 2012
Title: Architecture of the Nuclease Module of the Yeast Ccr4-not Complex: The not1-Caf1-Ccr4 Interaction.
Authors: Basquin, J. / Roudko, V.V. / Rode, M. / Basquin, C. / Seraphin, B. / Conti, E.
History
DepositionAug 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
B: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,90931
Polymers137,1972
Non-polymers5,71229
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-136 kcal/mol
Surface area47130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.097, 164.507, 86.141
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 / CELL DIVISION CYCLE PROTEIN 39 / NOT1


Mass: 68598.695 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 151-753
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE S288C (yeast) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS STAR / References: UniProt: P25655
#2: Chemical...
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Au

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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: 2.85 Å3/Da / Density % sol: 56.8 % / Description: NONE
Crystal growpH: 7.2 / Details: 2.8 M NACL AND 50 MM TRIS PH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03966
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03966 Å / Relative weight: 1
ReflectionResolution: 2.8→47.7 Å / Num. obs: 37032 / % possible obs: 99.5 % / Observed criterion σ(I): 2.6 / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.6 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.801→46.05 Å / SU ML: 0.44 / σ(F): 1 / Phase error: 33.1 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2757 1855 5 %
Rwork0.2376 --
obs0.2396 37032 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.276 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.103 Å20 Å2-19.3617 Å2
2---18.0324 Å20 Å2
3----3.0706 Å2
Refinement stepCycle: LAST / Resolution: 2.801→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8381 0 29 0 8410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098634
X-RAY DIFFRACTIONf_angle_d1.26711696
X-RAY DIFFRACTIONf_dihedral_angle_d16.3033149
X-RAY DIFFRACTIONf_chiral_restr0.0841379
X-RAY DIFFRACTIONf_plane_restr0.0051488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8007-2.87640.44311410.3722661X-RAY DIFFRACTION97
2.8764-2.9610.41551410.34892685X-RAY DIFFRACTION100
2.961-3.05660.39611440.31922732X-RAY DIFFRACTION100
3.0566-3.16580.35261400.27662647X-RAY DIFFRACTION100
3.1658-3.29250.30041430.26292730X-RAY DIFFRACTION100
3.2925-3.44230.32921450.25742747X-RAY DIFFRACTION100
3.4423-3.62370.25821400.23182653X-RAY DIFFRACTION100
3.6237-3.85070.27791410.23482688X-RAY DIFFRACTION100
3.8507-4.14780.2521440.2132719X-RAY DIFFRACTION100
4.1478-4.56490.2441440.19052732X-RAY DIFFRACTION100
4.5649-5.22460.25581420.20542713X-RAY DIFFRACTION100
5.2246-6.57940.29391440.27152722X-RAY DIFFRACTION100
6.5794-46.05630.21151460.20982748X-RAY DIFFRACTION100
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)
10.8894-0.49320.47071.6057-0.04130.91650.0733-0.0726-0.17270.04640.0068-0.04720.20720.0242-0.01970.30580.212-0.1799-0.36690.1682-0.0232-30.1577-0.4975-44.0242
21.1545-1.01811.09995.161-3.4824.90850.0929-0.0423-0.1063-0.44720.14140.3121-0.0871-0.1861-0.24060.5021-0.0761-0.1860.32780.01010.5729-15.9997-44.0144-0.2865
31.10340.61440.49753.7452-1.43973.2509-0.05880.18970.1925-0.06430.0717-0.0917-0.4556-0.13240.07070.2403-0.0474-0.06220.1285-0.04290.31983.6167-37.18931.3276
41.5862-1.09551.18163.7415-2.07453.0146-0.0258-0.2175-0.33230.6440.1367-0.28040.0608-0.1357-0.15140.40230-0.13030.1902-0.00450.4956-19.53426.5808-8.53
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 183:464)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 465:746)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 183:463)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 464:746)

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