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- PDB-4c0e: Structure of the NOT1 superfamily homology domain from Chaetomium... -

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Basic information

Entry
Database: PDB / ID: 4c0e
TitleStructure of the NOT1 superfamily homology domain from Chaetomium thermophilum
ComponentsNOT1
KeywordsGENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / HYDROLASE / TRANSCRIPTION
Function / homology
Function and homology information


CCR4-NOT core complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body / molecular adaptor activity / negative regulation of translation / nucleus
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #790 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #800 / 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 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #790 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #800 / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
General negative regulator of transcription subunit 1
Similarity search - Component
Biological speciesCHAETOMIUM THERMOPHILUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsChen, Y. / Boland, A. / 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 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag
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: NOT1
B: NOT1
C: NOT1
D: NOT1


Theoretical massNumber of molelcules
Total (without water)239,9324
Polymers239,9324
Non-polymers00
Water00
1
A: NOT1


Theoretical massNumber of molelcules
Total (without water)59,9831
Polymers59,9831
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NOT1


Theoretical massNumber of molelcules
Total (without water)59,9831
Polymers59,9831
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NOT1


Theoretical massNumber of molelcules
Total (without water)59,9831
Polymers59,9831
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NOT1


Theoretical massNumber of molelcules
Total (without water)59,9831
Polymers59,9831
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.750, 127.220, 130.200
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NOT1


Mass: 59983.105 Da / Num. of mol.: 4
Fragment: NOT1 SUPERFAMILY HOMOLOGY DOMAIN, RESIDUES 1676-2193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G0SAL9
Has protein modificationY
Sequence detailsTHE TEN N-TERMINAL RESIDUES REMAIN FROM THE INCOMPLETELY CLEAVED 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: 2.8 Å3/Da / Density % sol: 56 %
Description: SELENIUM SITES WERE IDENTIFIED IN DATA SET 2, COLLECTED AT 0.97925 A, PEAK DATA AT THE SE EDGE IN SG19.
Crystal growpH: 6
Details: 100MM MES PH=6.0, 180MM MGCL2, 5% PEG20000, 10MM PROLINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97925
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 3.2→90.9 Å / Num. obs: 41851 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 76.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

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

Resolution: 3.2→63.61 Å / SU ML: 0.41 / σ(F): 1.36 / Phase error: 27.74 / Stereochemistry target values: ML
Details: SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1674, 1682, 1715, 1801, 1802, 1804, 1867, 1880, 1981, 1996, 2001, 2005, 2031, 2035, 2133, 2141, 2142, ...Details: SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1674, 1682, 1715, 1801, 1802, 1804, 1867, 1880, 1981, 1996, 2001, 2005, 2031, 2035, 2133, 2141, 2142, 2163, 2170, 2174, 2175, 2178, 2181. CHAIN B, RESIDUES 1673, 1682, 1715, 1750, 1801, 1802, 1804, 1880, 1960, 1962, 1973, 1976, 1981, 1982, 2001, 2004, 2005, 2013, 2021, 2026, 2032, 2035, 2036, 2038, 2062, 2064, 2070, 2077, 2123, 2125, 2128, 2163, 2170, 2171, 2175, 2191. CHAIN C, RESIDUES 1666, 1696, 1700, 1701, 1702, 1720, 1721, 1722, 1737, 1770, 1772, 1831, 1867, 1880, 1960, 1963, 1973, 1976, 1982, 2001, 2005, 2013, 2014, 2025, 2027, 2038, 2123, 2128, 2145, 2172, 2174, 2175, 2176, 2178, 2183, 2186, 2190, 2191. CHAIN D, RESIDUES 1670, 1696, 1700, 1701, 1720, 1721, 1722, 1770, 1772, 1774, 1775, 1867, 1880, 1969, 1973, 1975, 1976, 1981, 1983, 1996, 2001, 2009, 2013, 2025, 2026, 2035, 2038, 2055, 2062, 2064, 2066, 2123, 2124, 2128, 2130, 2133, 2138, 2141, 2145, 2163, 2168, 2170, 2171, 2172, 2175, 2176, 2178, 2180, 2183, 2190. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 1771 TO 1777, 2027 TO 2030. CHAIN B, RESIDUES 1770 TO 1777, 2027 TO 2031, 2092, 2093. CHAIN C, RESIDUES 1774 TO 1776, 2028 TO 2033, 2092, 2093. CHAIN D, RESIDUES 1776, 2027 TO 2033, 2091 TO 2093.
RfactorNum. reflection% reflection
Rfree0.2586 2110 5.1 %
Rwork0.2168 --
obs0.2189 41820 99.87 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.352 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 87.6 Å2
Baniso -1Baniso -2Baniso -3
1-17.8646 Å20 Å221.4607 Å2
2---15.2439 Å20 Å2
3----2.6208 Å2
Refinement stepCycle: LAST / Resolution: 3.2→63.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15737 0 0 0 15737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216116
X-RAY DIFFRACTIONf_angle_d0.52621945
X-RAY DIFFRACTIONf_dihedral_angle_d11.3015632
X-RAY DIFFRACTIONf_chiral_restr0.0352531
X-RAY DIFFRACTIONf_plane_restr0.0032828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.27450.35971200.30962640X-RAY DIFFRACTION100
3.2745-3.35640.31181510.27742657X-RAY DIFFRACTION100
3.3564-3.44710.32671450.26482611X-RAY DIFFRACTION100
3.4471-3.54850.29321410.26172646X-RAY DIFFRACTION100
3.5485-3.66310.27931420.23572623X-RAY DIFFRACTION100
3.6631-3.7940.25281490.22912630X-RAY DIFFRACTION100
3.794-3.94590.27421230.21452641X-RAY DIFFRACTION100
3.9459-4.12540.2711290.20912664X-RAY DIFFRACTION100
4.1254-4.34290.2421420.19192670X-RAY DIFFRACTION100
4.3429-4.61490.24431460.18362617X-RAY DIFFRACTION100
4.6149-4.97110.22921440.19082641X-RAY DIFFRACTION100
4.9711-5.47110.22191220.20442678X-RAY DIFFRACTION100
5.4711-6.26220.24561680.24132625X-RAY DIFFRACTION100
6.2622-7.88730.2841550.22362662X-RAY DIFFRACTION100
7.8873-63.62250.22881330.19312705X-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)
11.8440.0705-0.63283.1149-1.02112.47550.01210.18750.1425-0.23650.0408-0.2015-0.25430.2572-0.02520.1393-0.01030.00290.11650.00540.092421.1248-14.455226.7127
22.55081.7008-1.50643.551-1.38952.4071-0.1085-0.1253-0.18950.16130.08020.09240.1296-0.06530.02930.3114-0.0042-0.03910.3302-0.0250.251313.606812.173837.7375
31.231-0.4861-1.311.53211.48615.56550.1122-0.2060.21570.17250.05140.0688-0.2866-0.0823-0.14780.3659-0.03570.03830.1989-0.010.3267.997348.500343.7095
44.1759-1.8333-2.40482.6461.4763.0505-0.05830.1384-0.1498-0.1166-0.02250.08060.00490.21460.06210.2757-0.0373-0.02120.21160.04270.332123.690676.707818.9037
53.56280.7326-0.43033.95730.0073.56790.1481-0.9285-0.22821.0364-0.27840.00180.4430.30670.10440.8085-0.00170.03520.69290.14330.336119.1191-33.623764.8586
63.7772-0.7999-0.24444.80170.71243.55950.070.05020.1667-0.3976-0.0397-0.7145-0.20560.80460.02620.3229-0.07860.02960.61570.02770.476247.608531.462720.8368
72.98640.6867-0.77484.6295-0.1493.6808-0.0730.57650.2527-0.43770.11740.03610.013-0.0226-0.05520.4419-0.0327-0.0210.42880.07960.326412.984344.19011.7739
82.2624-0.0013-0.43272.5616-0.39072.05410.1461-0.03820.00520.4364-0.03291.05980.1277-0.6455-0.16990.4663-0.15990.29530.5044-0.05161.1583-12.633381.063540.5636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND ((RESSEQ 1674:1961))
2X-RAY DIFFRACTION2CHAIN B AND ((RESSEQ 1674:1961))
3X-RAY DIFFRACTION3CHAIN C AND ((RESSEQ 1674:1961))
4X-RAY DIFFRACTION4CHAIN D AND ((RESSEQ 1674:1961))
5X-RAY DIFFRACTION5CHAIN A AND ((RESSEQ 1987:2193))
6X-RAY DIFFRACTION6CHAIN B AND ((RESSEQ 1987:2193))
7X-RAY DIFFRACTION7CHAIN C AND ((RESSEQ 1987:2193))
8X-RAY DIFFRACTION8CHAIN D AND ((RESSEQ 1987:2193))

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