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- PDB-4cqo: Structure of the human CNOT1 superfamily homology domain in compl... -

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Basic information

Entry
Database: PDB / ID: 4cqo
TitleStructure of the human CNOT1 superfamily homology domain in complex with a Nanos1 peptide
Components
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
  • NANOS HOMOLOG 1
KeywordsGENE REGULATION / TRANSLATION / DEADENYLATION / TRANSLATIONAL REPRESSION / PROTEIN COMPLEX / DEVELOPMENT / SHORT LINEAR MOTIF
Function / homology
Function and homology information


cerebellar neuron development / positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / epithelial cell migration / 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 ...cerebellar neuron development / positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / epithelial cell migration / 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 / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / tissue homeostasis / Deadenylation of mRNA / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / peroxisomal membrane / 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 / post-transcriptional regulation of gene expression / oogenesis / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / translation repressor activity / regulation of cell growth / nuclear estrogen receptor binding / P-body / cell migration / molecular adaptor activity / negative regulation of translation / protein domain specific binding / mRNA binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / RNA binding / extracellular space / zinc ion binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Nanos/Xcat2 / Zinc finger, nanos-type / Nanos domain superfamily / Nanos RNA binding domain / Zinc finger nanos-type profile. / 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 ...Nanos/Xcat2 / Zinc finger, nanos-type / Nanos domain superfamily / Nanos RNA binding domain / Zinc finger nanos-type profile. / 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
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / Nanos homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRaisch, T. / Jonas, S. / Weichenrieder, O. / Bhandari, D. / Izaurralde, E.
CitationJournal: Genes Dev. / Year: 2014
Title: Structural Basis for the Nanos-Mediated Recruitment of the Ccr4-not Complex and Translational Repression
Authors: Bhandari, D. / Raisch, T. / Weichenrieder, O. / Jonas, S. / Izaurralde, E.
History
DepositionFeb 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: 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

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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: NANOS HOMOLOG 1
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
D: NANOS HOMOLOG 1


Theoretical massNumber of molelcules
Total (without water)126,8934
Polymers126,8934
Non-polymers00
Water1,11762
1
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
D: NANOS HOMOLOG 1


Theoretical massNumber of molelcules
Total (without water)63,4462
Polymers63,4462
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-10 kcal/mol
Surface area24360 Å2
MethodPISA
2
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
B: NANOS HOMOLOG 1


Theoretical massNumber of molelcules
Total (without water)63,4462
Polymers63,4462
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-10 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.530, 167.330, 112.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9999, 0.0024, -0.0103), (0.0024, -1, -0.0005), (-0.0103, 0.0005, -0.9999)0.1368, 11.2409, 56.3009
2given(0.9999, -0.0101, -0.0029), (-0.01, -0.9996, 0.0247), (-0.0031, -0.0247, -0.9997)0.3167, 10.6913, 57.0147

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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


Mass: 61545.117 Da / Num. of mol.: 2
Fragment: NOT1 SUPERFAMILY HOMOLOGY DOMAIN, RESIDUES 1833-2362
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/peptide NANOS HOMOLOG 1 / NOS-1 / EC_REP1A


Mass: 1901.145 Da / Num. of mol.: 2 / Fragment: CNOT1 INTERACTING MOTIF, RESIDUES 40-56 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q8WY41
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST SIX RESIDUES (GPHMLE) REMAIN FROM THE 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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 7 / Details: 0.7 M SUCCINIC ACID SODIUM SALT, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.8→48.52 Å / Num. obs: 45219 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 47.98 Å2 / Rsym value: 0.16 / Net I/σ(I): 11.8
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 2.4 / Rsym value: 1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.3_1479)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C0D, CHAIN A

4c0d


Resolution: 2.8→48.452 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 32.45 / Stereochemistry target values: ML
Details: RESIDUES A 1827-1841, A 1917-1924, A 2083-2084, B 55-56, C 1827-1841, C 1922-1925 AND D 54-56 ARE DISORDERED. THE FOLLOWING RESIDUES WERE BUILT AS STUBS. CHAIN A 1842, 1870, 1914, 1916, ...Details: RESIDUES A 1827-1841, A 1917-1924, A 2083-2084, B 55-56, C 1827-1841, C 1922-1925 AND D 54-56 ARE DISORDERED. THE FOLLOWING RESIDUES WERE BUILT AS STUBS. CHAIN A 1842, 1870, 1914, 1916, 1931, 1952, 2059, CHAIN C 1842, 1870, 1927, 1931, 2059, CHAIN D 52
RfactorNum. reflection% reflection
Rfree0.2427 2294 5.1 %
Rwork0.2216 --
obs0.2227 45010 99.1 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.22 Å2
Baniso -1Baniso -2Baniso -3
1-78.23 Å20 Å20 Å2
2--29.55 Å20 Å2
3---50.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8518 0 0 62 8580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038788
X-RAY DIFFRACTIONf_angle_d0.62811965
X-RAY DIFFRACTIONf_dihedral_angle_d11.4563214
X-RAY DIFFRACTIONf_chiral_restr0.0231362
X-RAY DIFFRACTIONf_plane_restr0.0031527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.8610.47051430.35132600X-RAY DIFFRACTION99
2.861-2.92750.35291400.30972648X-RAY DIFFRACTION99
2.9275-3.00070.25861280.27192617X-RAY DIFFRACTION99
3.0007-3.08190.29671670.26582596X-RAY DIFFRACTION99
3.0819-3.17250.33691440.27252617X-RAY DIFFRACTION99
3.1725-3.27490.26721340.26352662X-RAY DIFFRACTION99
3.2749-3.39190.27931370.24192649X-RAY DIFFRACTION99
3.3919-3.52770.25231270.23372661X-RAY DIFFRACTION99
3.5277-3.68820.24941370.22952644X-RAY DIFFRACTION99
3.6882-3.88260.26131370.22562687X-RAY DIFFRACTION99
3.8826-4.12570.2391590.19942658X-RAY DIFFRACTION100
4.1257-4.4440.19891540.1832654X-RAY DIFFRACTION100
4.444-4.89090.19341630.1782701X-RAY DIFFRACTION100
4.8909-5.59770.24881400.20472732X-RAY DIFFRACTION100
5.5977-7.04910.23651490.21772750X-RAY DIFFRACTION100
7.0491-48.45920.16721350.1882840X-RAY DIFFRACTION98
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)
12.6160.6450.7816.60221.79682.62230.0761-0.07860.06740.5695-0.0972-0.1095-0.0626-0.08640.00240.7815-0.0326-0.08330.3819-0.02050.406217.924436.014154.2347
22.6849-2.0419-1.44485.4152.01654.14530.07760.0567-0.01330.2185-0.105-0.0904-0.1124-0.1048-0.04240.5455-0.032-0.1060.3320.03170.365321.06196.698142.3933
31.4935-0.43541.05262.3754-0.39473.6421-0.1029-0.1738-0.02250.35580.0342-0.08920.3079-0.16930.05020.6061-0.0149-0.04210.35970.0260.413524.08-16.13543.6093
42.238-1.2174-0.54335.62961.22873.34310.10320.0778-0.048-0.1364-0.0444-0.3180.213-0.1623-0.05050.34710.0210.05650.334-0.02580.265417.2766-24.7522.1522
51.82420.4866-0.33853.3152-1.333.4816-0.04260.01970.09340.0932-0.0046-0.2442-0.16640.05830.03130.2564-0.0138-0.04530.25440.00760.336724.066527.45212.4683
65.48523.76244.4112.9893.21113.6321-0.0252-0.4109-0.13850.3843-0.27580.19051.8710.27680.41990.8393-0.04460.02630.4622-0.00120.222616.7619-19.971820.6049
76.81-5.5309-5.07284.49164.11973.7767-1.27731.87430.91071.5240.20940.011-0.42860.00260.90650.8116-0.1195-0.18160.54690.05520.57238.6763-11.557916.046
82.4371-2.1542-2.82868.02993.40538.7091-0.096-0.0307-0.1354-0.01630.23440.3663-2.44910.1136-0.01050.98490.0726-0.21810.4193-0.03590.445716.892231.363635.5627
95.77085.76931.93445.76841.93782.054-0.4012-0.0844-2.9179-0.46260.3357-0.6262.0843-1.25770.13411.3186-0.1698-0.220.62010.14240.95079.39123.446340.5142
101.22431.10550.63754.18531.62362.85870.1196-0.1149-0.06390.2353-0.0732-0.45960.06590.2522-0.03060.2765-0.00360.04930.32150.0540.294520.70384.712313.7501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1842 THROUGH 2025 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 2026 THROUGH 2154 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 2155 THROUGH 2361 )
4X-RAY DIFFRACTION4CHAIN C AND (RESID 1842 THROUGH 2025 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 2155 THROUGH 2361 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 40 THROUGH 47 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 48 THROUGH 54 )
8X-RAY DIFFRACTION8CHAIN D AND (RESID 40 THROUGH 47 )
9X-RAY DIFFRACTION9CHAIN D AND (RESID 48 THROUGH 53 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 2026 THROUGH 2154 )

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