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- PDB-4crv: Complex of human CNOT9 and CNOT1 including two tryptophans -

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Basic information

Entry
Database: PDB / ID: 4crv
TitleComplex of human CNOT9 and CNOT1 including two tryptophans
Components
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
  • CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOG
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 / 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 / sex differentiation / negative regulation of intracellular estrogen receptor signaling pathway ...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 / sex differentiation / 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 / epidermal growth factor receptor binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of peptidyl-serine phosphorylation / nuclear estrogen receptor binding / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / molecular adaptor activity / transcription coactivator activity / negative regulation of translation / protein domain specific binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / extracellular space / RNA binding / nucleus / membrane / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / : / 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 9 / Cell differentiation family, Rcd1-like / : / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
TRYPTOPHAN / 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: 2.05 Å
AuthorsBoland, A. / Chen, Y. / 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 1.1Jun 18, 2014Group: Database references
Revision 1.2Dec 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)60,5434
Polymers60,2472
Non-polymers2962
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-25 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.070, 66.810, 71.990
Angle α, β, γ (deg.)90.00, 100.22, 90.00
Int Tables number5
Space group name H-MC121

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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 / 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-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 61 % / Description: NONE
Crystal growpH: 6
Details: 0.1M MES (PH=6.0), 11% PEG6000, 0.05M MG-CHLORIDE, 0.04M L-TRYPTOPHAN

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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: Aug 19, 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: 2.05→61.1 Å / Num. obs: 45149 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 43 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.9
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.79 / % 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 4CRU

4cru


Resolution: 2.05→61.138 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 27.12 / Stereochemistry target values: ML
Details: TLS PARAMETERS WERE REFINED. SIDE CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1353, 1399, 1478, 1586, 1587. CHAIN B, RESIDUES 15, 17, 169. THE FOLLOWING ...Details: TLS PARAMETERS WERE REFINED. SIDE CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1353, 1399, 1478, 1586, 1587. CHAIN B, RESIDUES 15, 17, 169. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 1350 TO 1352, 1588 TO 1602, 1604 TO 1607. CHAIN B, RESIDUES 13, 14.
RfactorNum. reflection% reflection
Rfree0.2154 2254 5 %
Rwork0.176 --
obs0.178 45057 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.3 Å2
Refinement stepCycle: LAST / Resolution: 2.05→61.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4009 0 21 148 4178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064105
X-RAY DIFFRACTIONf_angle_d0.8835565
X-RAY DIFFRACTIONf_dihedral_angle_d13.4911552
X-RAY DIFFRACTIONf_chiral_restr0.033648
X-RAY DIFFRACTIONf_plane_restr0.005713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.09460.31961440.30072621X-RAY DIFFRACTION98
2.0946-2.14330.31441370.26762663X-RAY DIFFRACTION99
2.1433-2.19690.31221370.23962610X-RAY DIFFRACTION99
2.1969-2.25630.25541430.22482650X-RAY DIFFRACTION99
2.2563-2.32270.29061370.21452669X-RAY DIFFRACTION99
2.3227-2.39770.24051430.20062659X-RAY DIFFRACTION99
2.3977-2.48340.25181350.1852681X-RAY DIFFRACTION99
2.4834-2.58280.21791430.18222636X-RAY DIFFRACTION99
2.5828-2.70040.20371390.18312670X-RAY DIFFRACTION100
2.7004-2.84270.25541420.18862657X-RAY DIFFRACTION100
2.8427-3.02080.22931450.19452699X-RAY DIFFRACTION100
3.0208-3.25410.26541400.2042682X-RAY DIFFRACTION100
3.2541-3.58150.24061420.18312692X-RAY DIFFRACTION100
3.5815-4.09970.20161390.16492719X-RAY DIFFRACTION100
4.0997-5.16470.16541450.14462719X-RAY DIFFRACTION100
5.1647-61.16510.18131430.15182776X-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)
12.83810.2372-0.84170.69760.16440.7841-0.22010.4222-1.13980.36570.1655-0.71190.68360.58260.01170.8730.0932-0.18710.7269-0.00491.011946.3118-13.517935.8989
22.07310.42390.91021.20230.15031.80130.0781-0.25830.13210.26390.0059-0.24730.22190.18460.01620.47530.0107-0.03030.42220.00160.462630.5297-0.688635.6749
30.58730.51380.01520.68690.15180.9490.06850.0755-1.33130.4447-0.0740.42740.5989-0.22220.0620.7292-0.12250.07110.62230.02540.671311.8888-10.170533.3038
40.78851.18660.49812.01841.04120.6811-0.0368-0.08110.10290.0785-0.0977-0.1024-0.10560.09450.00421.45010.10490.14781.02320.19751.256239.070529.870913.6925
51.871-0.1573-0.0341.3030.28421.6496-0.10260.2767-0.1461-0.0130.01620.14460.2345-0.226500.3784-0.03810.00530.3996-0.05920.405816.6149-3.961818.3725
61.46570.8964-0.75512.1405-1.26541.9174-0.0150.28080.2402-0.22730.0664-0.0891-0.157-0.03300.533-0.02980.03080.46240.0370.443130.272717.90874.3176
70.2488-0.07510.41390.08470.03761.1132-0.0856-0.02130.02310.1894-0.0006-0.0071-0.0243-0.0761-0.00141.0442-0.0938-0.10650.9025-0.02190.725635.877416.94718.0878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1353 THROUGH 1386 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1387 THROUGH 1552 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1553 THROUGH 1587 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1603 THROUGH 1603 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 15 THROUGH 149 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 150 THROUGH 285)
7X-RAY DIFFRACTION7CHAIN B AND (RESID 1286 THROUGH 1286)

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