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- PDB-5fu6: NOT module of the human CCR4-NOT complex (Crystallization mutant) -

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Basic information

Entry
Database: PDB / ID: 5fu6
TitleNOT module of the human CCR4-NOT complex (Crystallization mutant)
Components
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
KeywordsGENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / TRANSCRIPTION / TRANSLATIONAL REPRESSION
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / armadillo repeat domain binding / CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / positive regulation of mRNA catabolic process / negative regulation of retinoic acid receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / miRNA-mediated post-transcriptional gene silencing ...positive regulation of cytoplasmic mRNA processing body assembly / armadillo repeat domain binding / CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / positive regulation of mRNA catabolic process / negative regulation of retinoic acid receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / miRNA-mediated post-transcriptional gene silencing / trophectodermal cell differentiation / 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 / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator activity / P-body / regulation of translation / positive regulation of cold-induced thermogenesis / molecular adaptor activity / negative regulation of translation / 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 / nucleoplasm / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CCR4-NOT complex subunit 2/3/5, C-terminal domain / CCR4-Not complex component, Not N-terminal domain / NOT2/NOT3/NOT5, C-terminal / 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 / : / CCR4-NOT transcription complex subunit 1, N-terminal domain ...CCR4-NOT complex subunit 2/3/5, C-terminal domain / CCR4-Not complex component, Not N-terminal domain / NOT2/NOT3/NOT5, C-terminal / 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 / : / CCR4-NOT transcription complex subunit 1, N-terminal domain / CCR4-NOT transcription complex subunit 1, NOT1_connector / : / 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
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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, E, F ARE ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURES OF CHAINS B, C, E, F ARE BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED EACH FOR CHAINS B, C, E, F.

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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: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
E: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
F: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3


Theoretical massNumber of molelcules
Total (without water)205,6666
Polymers205,6666
Non-polymers00
Water00
1
D: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
E: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
F: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3


Theoretical massNumber of molelcules
Total (without water)102,8333
Polymers102,8333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13710 Å2
ΔGint-82.7 kcal/mol
Surface area37850 Å2
MethodPISA
2
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
B: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3


Theoretical massNumber of molelcules
Total (without water)102,8333
Polymers102,8333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-81.5 kcal/mol
Surface area37990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.980, 135.320, 101.330
Angle α, β, γ (deg.)90.00, 107.67, 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 / CNOT1


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 / CNOT2


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 / CNOT3


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
Sequence detailsCHAIN A, D. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN B, E. THE SIX N- ...CHAIN A, D. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN B, E. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN C, F. 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: 50.5 % / Description: NONE
Crystal growpH: 5.5
Details: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CITRATE PH 5.5, 10 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99982
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2015 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99982 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 43109 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.26 % / Biso Wilson estimate: 81.37 Å2 / Rsym value: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.27 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.63 / % possible all: 99.7

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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: 2.9→48.24 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9284 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.349
Details: THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, 1833 TO 1841, 2005 TO 2009. CHAIN D, 1833 TO 1841, 2004 TO 2007. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN B, ...Details: THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, 1833 TO 1841, 2005 TO 2009. CHAIN D, 1833 TO 1841, 2004 TO 2007. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN B, RESIDUE 489. CHAIN D, RESIDUE 2008. CHAIN E, RESIDUE 531.
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 2200 5.1 %RANDOM
Rwork0.1807 ---
obs0.1827 43108 99.57 %-
Displacement parametersBiso mean: 83.94 Å2
Baniso -1Baniso -2Baniso -3
1--6.0947 Å20 Å20.0698 Å2
2--14.7266 Å20 Å2
3----8.6319 Å2
Refine analyzeLuzzati coordinate error obs: 0.346 Å
Refinement stepCycle: LAST / Resolution: 2.9→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14109 0 0 0 14109
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114521HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.119731HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4951SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes352HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2081HARMONIC5
X-RAY DIFFRACTIONt_it14521HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion20.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1844SEMIHARMONIC5
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_contact16800SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 183 5.74 %
Rwork0.2288 3003 -
all0.2298 3186 -
obs--99.78 %
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)
11.9631.1594-0.57232.5268-0.95870.81780.1194-0.1571-0.02360.2318-0.12160.1824-0.16040.0380.0022-0.1080.0311-0.0017-0.2046-0.1046-0.145636.403-12.502239.9704
21.5735-0.1846-0.46050.06380.84760.49060.04910.6646-0.1139-0.2959-0.26730.1728-0.1476-0.3050.2182-0.07930.1959-0.18420.0045-0.1255-0.00398.3263-17.532723.9057
32.9545-0.4985-1.53270.94540.98061.6260.13390.3768-0.3916-0.0004-0.50640.50780.023-0.47240.3725-0.23880.002-0.0244-0.161-0.18330.10441.2283-22.872441.7912
41.6368-0.08061.13912.8728-1.84172.4581-0.02850.1646-0.0424-0.4264-0.1128-0.10240.24230.30450.1413-0.12730.06370.0657-0.312-0.0669-0.256913.9197-52.705111.0777
51.2048-0.46471.07190.02540.22511.53540.0028-0.422-0.09470.104-0.0030.2176-0.1089-0.49310.0002-0.0713-0.06060.0557-0.0512-0.0312-0.0186-18.6157-47.2316107.4814
60.6644-0.20130.15910.58480.6731.54150.04460.00830.196-0.198-0.27840.22-0.1564-0.48530.2338-0.04370.0419-0.1233-0.134-0.0002-0.022-13.8287-42.103888.9946
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

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