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- PDB-4cru: Complex of human CNOT9 and CNOT1 including one tryptophan -

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Basic information

Entry
Database: PDB / ID: 4cru
TitleComplex of human CNOT9 and CNOT1 including one tryptophan
Components
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
  • CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOGCellular differentiation
KeywordsGENE REGULATION / TNRC6 BINDING / MIRISC / MRNA SILENCING / MRNA DEADENYLATION / ARGONAUTE / TRANSCRIPTION
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 / sex 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 / sex differentiation / 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 / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / nuclear receptor coactivator activity / nuclear estrogen receptor binding / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / positive regulation of peptidyl-serine phosphorylation / negative regulation of translation / molecular adaptor activity / protein domain specific binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / extracellular space / RNA binding / membrane / nucleus / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / 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 9 / Cell differentiation family, Rcd1-like / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsChen, Y. / Boland, A. / Izaurralde, E. / Weichenrieder, O.
CitationJournal: Mol.Cell / Year: 2014
Title: A Ddx6-Cnot1 Complex and W-Binding Pockets in Cnot9 Reveal Direct Links between Mirna Target Recognition and Silencing
Authors: Chen, Y. / Boland, A. / Kuzuoglu-Ozturk, D. / Bawankar, P. / Loh, B. / Chang, C.T. / Weichenrieder, O. / Izaurralde, E.
History
DepositionMar 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Atomic model
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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: CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4314
Polymers60,2472
Non-polymers1842
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-31 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.800, 67.240, 72.300
Angle α, β, γ (deg.)90.00, 99.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

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Components

#1: Protein CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 / CNOT1 / CCR4-ASSOCIATED FACTOR 1 / NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 HOMOLOG / NOT1H / HNOT1


Mass: 29174.605 Da / Num. of mol.: 1 / Fragment: CNOT1 CN9BD DOMAIN, DUF3819, RESIDUES 1356-1607
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 CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOG / Cellular differentiation / CNOT9 / CAF40 HOMOLOGG / RCD-1 / CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 9 / RCD-1


Mass: 31072.189 Da / Num. of mol.: 1 / Fragment: CNOT9 ARM DOMAIN, RESIDUES 19-285
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: Q92600
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG OF CHAIN A. THE SIX N-TERMINAL RESIDUES ...THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG OF CHAIN A. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG OF CHAIN B.

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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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 6 / Details: 0.1M MES (PH=6.0), 8% PEG6000, 0.08M MG-CHLORIDE

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2013 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→76.3 Å / Num. obs: 87658 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 26.7 Å2 / Rsym value: 0.02 / Net I/σ(I): 19.8
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.64 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FV2 CHAIN A

2fv2


Resolution: 1.65→76.307 Å / SU ML: 0.16 / σ(F): 1.99 / Phase error: 19.17 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. TLS PARAMETERS WERE REFINED. SIDE CHAINS OF THE FOLLOWING RESIDUES HAVE DOUBLE CONFORMATIONS. CHAIN A, RESIDUES 1360, 1497, 1532, 1539, 1552, ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. TLS PARAMETERS WERE REFINED. SIDE CHAINS OF THE FOLLOWING RESIDUES HAVE DOUBLE CONFORMATIONS. CHAIN A, RESIDUES 1360, 1497, 1532, 1539, 1552, 1558. CHAIN B, RESIDUES 133. SIDE CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1478, 1587, 1588, 1601. CHAIN B, RESIDUES 16, 18. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 1350, 1589 TO 1600, 1606-1607. CHAIN B, RESIDUES 13 TO 15.
RfactorNum. reflection% reflection
Rfree0.1788 4388 5 %
Rwork0.1596 --
obs0.1606 87644 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.5 Å2
Refinement stepCycle: LAST / Resolution: 1.65→76.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 12 474 4540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114200
X-RAY DIFFRACTIONf_angle_d1.2665699
X-RAY DIFFRACTIONf_dihedral_angle_d14.3611610
X-RAY DIFFRACTIONf_chiral_restr0.053660
X-RAY DIFFRACTIONf_plane_restr0.008732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66880.30891460.27312708X-RAY DIFFRACTION99
1.6688-1.68840.28781430.26262745X-RAY DIFFRACTION99
1.6884-1.7090.31441460.24882750X-RAY DIFFRACTION99
1.709-1.73060.26071430.22922789X-RAY DIFFRACTION99
1.7306-1.75340.27361490.22052757X-RAY DIFFRACTION100
1.7534-1.77740.22311430.2182717X-RAY DIFFRACTION100
1.7774-1.80280.21181470.2042785X-RAY DIFFRACTION99
1.8028-1.82970.23051460.19882780X-RAY DIFFRACTION100
1.8297-1.85830.2021460.19472779X-RAY DIFFRACTION100
1.8583-1.88880.20691420.19112738X-RAY DIFFRACTION99
1.8888-1.92140.2021480.18732778X-RAY DIFFRACTION99
1.9214-1.95630.21831460.18132768X-RAY DIFFRACTION100
1.9563-1.99390.20741450.17522741X-RAY DIFFRACTION100
1.9939-2.03460.18191460.1672798X-RAY DIFFRACTION100
2.0346-2.07890.18541470.16152760X-RAY DIFFRACTION100
2.0789-2.12720.19771470.15932800X-RAY DIFFRACTION100
2.1272-2.18040.16451470.1592790X-RAY DIFFRACTION100
2.1804-2.23940.1971450.15282751X-RAY DIFFRACTION100
2.2394-2.30530.17051460.15292765X-RAY DIFFRACTION100
2.3053-2.37970.16131450.14562801X-RAY DIFFRACTION100
2.3797-2.46480.16541470.14152764X-RAY DIFFRACTION100
2.4648-2.56340.17821470.14422782X-RAY DIFFRACTION100
2.5634-2.68010.14891480.14682799X-RAY DIFFRACTION100
2.6801-2.82140.16751470.15092794X-RAY DIFFRACTION100
2.8214-2.99820.17791470.15632783X-RAY DIFFRACTION100
2.9982-3.22970.17471460.16132775X-RAY DIFFRACTION99
3.2297-3.55470.21221470.15562793X-RAY DIFFRACTION99
3.5547-4.06910.16351470.15282782X-RAY DIFFRACTION99
4.0691-5.12640.13731480.13732815X-RAY DIFFRACTION99
5.1264-76.3890.17611510.16292869X-RAY DIFFRACTION99
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)
10.6307-0.0692-0.24420.8122-0.19790.40070.06570.3369-0.4558-0.1155-0.0355-0.2840.18020.151800.46850.0495-0.09890.3567-0.04230.472545.6746-11.807835.3131
21.4358-0.17311.06251.09090.02571.0840.04110.02620.17910.0803-0.0184-0.2670.06680.17960.00350.22670.0195-0.03120.22890.00050.267334.23560.975835.4551
31.25920.45611.3761.86010.07311.54510.08440.5085-0.2109-0.0658-0.0886-0.45650.16790.34970.0010.25470.0555-0.0510.2960.01490.319945.4647-2.669832.3027
40.10180.02790.03230.1362-0.08870.10260.1354-0.87810.68570.32590.0674-0.0531-0.2182-0.1978-0.00050.2853-0.02910.02120.5943-0.07760.40514.35178.068946.9966
50.01660.02440.01660.04030.03930.02760.09320.29110.1951-0.0812-0.10530.228-0.1017-0.33520.00040.16690.02720.02390.37860.04520.2855-2.63487.373829.3582
60.51830.28220.09720.267-0.09810.4858-0.0167-0.0823-0.90130.25890.09570.33020.3248-0.2039-0.0190.3222-0.07620.0090.29520.01610.381412.2471-8.372233.4255
70.04080.0089-0.00240.0121-0.0080.00690.0951-0.03660.05580.07260.2044-0.1617-0.09370.1601-0.00020.9196-0.1504-0.04250.70920.2751.324741.799831.868514.715
81.6679-0.0636-0.27151.7995-0.03131.4465-0.02140.2173-0.1281-0.15960.00670.13760.2061-0.1264-0.00170.214-0.0227-0.02150.1949-0.0340.171717.3735-1.98218.6209
92.17710.9101-1.08062.7121-1.11042.768-0.01040.21520.1467-0.05460.04950.0359-0.10350.024100.3046-0.02360.01760.2720.03220.255530.269720.00554.6239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1351 THROUGH 1386 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1387 THROUGH 1476 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1477 THROUGH 1522 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1523 THROUGH 1542 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1543 THROUGH 1552 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 1553 THROUGH 1588 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 1601 THROUGH 1604 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 16 THROUGH 147 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 148 THROUGH 285 )

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