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- PDB-4c0g: Structure of the NOT-box domain of human CNOT3 -

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Basic information

Entry
Database: PDB / ID: 4c0g
TitleStructure of the NOT-box domain of human CNOT3
ComponentsCCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
KeywordsGENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / HYDROLASE / TRANSCRIPTION
Function / homology
Function and homology information


CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / P-body ...CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / P-body / positive regulation of cold-induced thermogenesis / regulation of DNA-templated transcription / nucleus / cytosol
Similarity search - Function
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 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBoland, A. / Chen, Y. / Raisch, T. / Jonas, S. / Izaurralde, E. / Weichenrieder, O.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure and Assembly of the not Module of the Human Ccr4-not Complex
Authors: Boland, A. / Chen, Y. / Raisch, T. / Jonas, S. / Kuzuoglu-Ozturk, D. / Wohlbold, L. / Weichenrieder, O. / Izaurralde, E.
History
DepositionAug 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Nov 20, 2013Group: Database references
Revision 1.4Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_source
Remark 700 SHEETS THE SHEET STRUCTURES OF CHAIN A, B, C, D, E, F ARE BIFURCATED. IN ORDER TO REPRESENT THIS ... SHEETS THE SHEET STRUCTURES OF CHAIN A, B, C, D, E, F ARE BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED EACH FOR CHAINS A, B, C, D, E, F.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
B: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
D: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
E: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
F: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3


Theoretical massNumber of molelcules
Total (without water)77,0286
Polymers77,0286
Non-polymers00
Water1,36976
1
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
D: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3


Theoretical massNumber of molelcules
Total (without water)25,6762
Polymers25,6762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-11.5 kcal/mol
Surface area13740 Å2
MethodPQS
2
B: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
E: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3


Theoretical massNumber of molelcules
Total (without water)25,6762
Polymers25,6762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-4.4 kcal/mol
Surface area13660 Å2
MethodPQS
3
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
F: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3


Theoretical massNumber of molelcules
Total (without water)25,6762
Polymers25,6762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-9.5 kcal/mol
Surface area13750 Å2
MethodPQS
Unit cell
Length a, b, c (Å)52.300, 97.570, 141.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3 / CCR4-ASSOCIATED FACTOR 3 / LEUKOCYTE RECEPTOR CLUSTER MEMBER 2 / CNOT3


Mass: 12837.923 Da / Num. of mol.: 6 / Fragment: NOT-BOX DOMAIN, RESIDUES 656-753
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: O75175
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FOUR 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: 3 Å3/Da / Density % sol: 59.1 %
Description: SELENIUM SITES WERE IDENTIFIED IN DATA SET 2, COLLECTED AT 0.97950 A, PEAK DATA AT THE SE EDGE.
Crystal growpH: 7.8
Details: 100 MM HEPES PH=7.8, 13% PEG4000, 2% GLYCEROL, 12% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00000, 0.97950
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2011 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
ReflectionResolution: 2.4→49.1 Å / Num. obs: 28972 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 54 Å2 / Rsym value: 0.05 / Net I/σ(I): 18.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.7 / % possible all: 99.8

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
SHELXphasing
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→49.058 Å / SU ML: 0.45 / σ(F): 1.36 / Phase error: 28.95 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUE 713. CHAIN B, RESIDUES 658, 730, 749. CHAIN C, RESIDUES ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUE 713. CHAIN B, RESIDUES 658, 730, 749. CHAIN C, RESIDUES 656, 689, 729, 748. CHAIN D, RESIDUES 658, 749. CHAIN E, RESIDUES 658, 748. CHAIN F, RESIDUES 665, 693, 750.
RfactorNum. reflection% reflection
Rfree0.2566 1477 5.1 %
Rwork0.2208 --
obs0.2226 28937 99.42 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.347 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso mean: 69.1 Å2
Baniso -1Baniso -2Baniso -3
1--20.1245 Å20 Å20 Å2
2---1.7364 Å20 Å2
3---21.8609 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 0 76 5060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025153
X-RAY DIFFRACTIONf_angle_d0.6156932
X-RAY DIFFRACTIONf_dihedral_angle_d15.9121850
X-RAY DIFFRACTIONf_chiral_restr0.044653
X-RAY DIFFRACTIONf_plane_restr0.002862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.45551310.37482438X-RAY DIFFRACTION99
2.4775-2.5660.36551570.33922448X-RAY DIFFRACTION100
2.566-2.66880.3771190.32342457X-RAY DIFFRACTION100
2.6688-2.79020.37911280.30372497X-RAY DIFFRACTION100
2.7902-2.93730.32031230.26642490X-RAY DIFFRACTION100
2.9373-3.12130.24651200.25142470X-RAY DIFFRACTION100
3.1213-3.36220.28371390.23312485X-RAY DIFFRACTION100
3.3622-3.70050.25181440.21912486X-RAY DIFFRACTION99
3.7005-4.23570.20911450.19442480X-RAY DIFFRACTION99
4.2357-5.33550.20421390.15952522X-RAY DIFFRACTION99
5.3355-49.06790.25671320.21232687X-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)
15.66760.68431.38894.599-0.83896.13270.42240.74440.6701-0.26950.02880.3815-0.9838-0.65480.01310.57020.14950.17730.59090.2090.569-34.1086-39.816227.7998
26.5512-0.6894-1.58319.1102-2.17325.3420.3177-0.5051.22880.40310.169-0.2896-0.79610.2583-0.30220.4361-0.05020.11950.3168-0.15630.4501-16.387613.78324.4571
34.35441.832.68473.95551.44352.41570.74831.6702-3.4395-0.77970.7074-0.09020.42331.1277-0.4980.58590.128-0.35510.1398-0.31061.41459.144-21.457216.2225
47.3346-2.0147-3.76024.47910.83676.6460.4123-0.80480.92080.12960.51-0.1595-0.60880.3971-0.80870.54330.03350.20130.39910.02470.5117-16.9755-39.888929.5638
52.38571.16141.9897.38020.28965.980.19550.27070.8907-0.11530.00430.8659-0.6153-0.1558-0.00460.54390.07210.22570.41040.11590.7221-33.357914.80152.4907
60.4717-0.0648-0.1394-0.04230.08870.73550.1344-0.5184-1.2144-0.1530.55161.44910.73780.36850.09830.5209-0.0297-0.22740.24830.10921.2259-7.8092-22.175718.012
70.7157-0.0935-1.16590.97910.1531.51780.22850.0057-0.06940.19280.01980.35860.2087-0.21190.00680.37020.00850.09980.55770.1150.4274-41.9775-50.324440.2518
88.9548-2.5602-4.58945.57020.54048.08620.48981.00780.3559-0.3276-0.4371-0.1958-0.1-0.2616-0.01950.3713-0.0211-0.02390.51840.0810.3278-9.051310.498-12.0015
93.72520.47174.05142.19450.6226.54620.2438-1.1672-1.10160.3745-0.00430.2364-0.0132-0.5085-0.25670.3559-0.00010.01880.51270.06580.536516.5155-13.952831.435
106.06330.3456-3.18585.4005-0.73856.53690.24450.94450.5362-0.32130.2411-0.02920.1007-0.0368-0.44280.37280.012-0.01790.46760.04980.2917-9.6-46.934714.4449
112.55560.0424-1.68243.37-0.5213.55260.4363-0.01460.38270.33-0.10560.60130.1329-0.3511-0.31170.34240.03740.06840.34390.05630.4227-41.81850.984211.2827
127.2134-1.27723.70622.8641-0.98254.54950.23990.5195-1.2058-0.0744-0.0452-0.0597-0.06210.0243-0.19320.29290.007-0.0130.2815-0.01120.5008-16.0403-10.66056.5096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND ((RESSEQ 658:695))
2X-RAY DIFFRACTION2CHAIN B AND ((RESSEQ 658:695))
3X-RAY DIFFRACTION3CHAIN C AND ((RESSEQ 658:695))
4X-RAY DIFFRACTION4CHAIN D AND ((RESSEQ 658:695))
5X-RAY DIFFRACTION5CHAIN E AND ((RESSEQ 658:695))
6X-RAY DIFFRACTION6CHAIN F AND ((RESSEQ 658:695))
7X-RAY DIFFRACTION7CHAIN A AND ((RESSEQ 696:745))
8X-RAY DIFFRACTION8CHAIN B AND ((RESSEQ 696:745))
9X-RAY DIFFRACTION9CHAIN C AND ((RESSEQ 696:745))
10X-RAY DIFFRACTION10CHAIN D AND ((RESSEQ 696:745))
11X-RAY DIFFRACTION11CHAIN E AND ((RESSEQ 696:745))
12X-RAY DIFFRACTION12CHAIN F AND ((RESSEQ 696:745))

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