[English] 日本語
Yorodumi
- PDB-6hon: Drosophila NOT4 CBM peptide bound to human CAF40 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hon
TitleDrosophila NOT4 CBM peptide bound to human CAF40
Components
  • CCR4-NOT transcription complex subunit 4, isoform L
  • CCR4-NOT transcription complex subunit 9
KeywordsGENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / HYDROLASE / TRANSCRIPTION / UBIQUITINATION
Function / homology
Function and homology information


CCR4-NOT core complex / CCR4-NOT complex / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / sex 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 / positive regulation of epidermal growth factor receptor signaling pathway ...CCR4-NOT core complex / CCR4-NOT complex / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / sex 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 / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / nuclear receptor coactivator activity / P-body / kinase binding / cytokine-mediated signaling pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / ubiquitin-protein transferase activity / positive regulation of peptidyl-serine phosphorylation / negative regulation of translation / protein ubiquitination / protein domain specific binding / protein homodimerization activity / protein-containing complex / RNA binding / membrane / nucleus / metal ion binding / cytosol
Similarity search - Function
CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / RING/Ubox like zinc-binding domain / CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / RNA recognition motif domain, eukaryote / RNA recognition motif / zinc finger / Zinc finger, CCCH-type ...CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / RING/Ubox like zinc-binding domain / CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / RNA recognition motif domain, eukaryote / RNA recognition motif / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Zinc finger RING-type profile. / RNA-binding domain superfamily / Zinc finger, RING-type / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 4, isoform L / CCR4-NOT transcription complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRaisch, T. / Izaurralde, E. / Weichenrieder, O.
CitationJournal: Genes Dev. / Year: 2019
Title: A conserved CAF40-binding motif in metazoan NOT4 mediates association with the CCR4-NOT complex.
Authors: Keskeny, C. / Raisch, T. / Sgromo, A. / Igreja, C. / Bhandari, D. / Weichenrieder, O. / Izaurralde, E.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CCR4-NOT transcription complex subunit 9
B: CCR4-NOT transcription complex subunit 4, isoform L
C: CCR4-NOT transcription complex subunit 9
D: CCR4-NOT transcription complex subunit 4, isoform L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1197
Polymers68,0254
Non-polymers943
Water1,15364
1
A: CCR4-NOT transcription complex subunit 9
B: CCR4-NOT transcription complex subunit 4, isoform L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1065
Polymers34,0122
Non-polymers943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-33 kcal/mol
Surface area14170 Å2
MethodPISA
2
C: CCR4-NOT transcription complex subunit 9
D: CCR4-NOT transcription complex subunit 4, isoform L


Theoretical massNumber of molelcules
Total (without water)34,0122
Polymers34,0122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-11 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.630, 90.320, 196.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-301-

NA

-
Components

#1: Protein CCR4-NOT transcription complex subunit 9 / Cell differentiation protein RQCD1 homolog / Rcd-1


Mass: 31072.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first six residues (GPHMLE) remain from the expression tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT9, RCD1, RQCD1 / Plasmid: PETMCN(PNEA) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q92600
#2: Protein/peptide CCR4-NOT transcription complex subunit 4, isoform L


Mass: 2940.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: M9PCL9
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.9 M K2HPO4, 0.3 M NaH2PO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2016 / 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: 2.2→50 Å / Num. obs: 39129 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 56.7 Å2 / CC1/2: 1 / Rsym value: 0.065 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.25 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2831 / CC1/2: 0.899 / Rsym value: 1.57

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fv2, chain A

2fv2


Resolution: 2.2→49.25 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9269 / SU R Cruickshank DPI: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.202 / SU Rfree Blow DPI: 0.173 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1907 4.87 %RANDOM
Rwork0.1928 ---
obs0.1947 39127 99.88 %-
Displacement parametersBiso mean: 81 Å2
Baniso -1Baniso -2Baniso -3
1--5.322 Å20 Å20 Å2
2---20.3523 Å20 Å2
3---25.6742 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 3 64 4805
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014828HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.046556HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1714SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes678HARMONIC5
X-RAY DIFFRACTIONt_it4828HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion17.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion650SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5597SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2755 123 4.34 %
Rwork0.2477 2709 -
all0.2488 2832 -
obs--99.79 %
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)
12.20930.192-0.79870.4747-0.16313.42670.04360.24190.21970.02590.0070.0414-0.5592-0.3431-0.0506-0.05590.1320.0218-0.15240.0165-0.18434.064593.8235210.52
24.3621-2.6806-1.79713.04331.88680.1201-0.0357-0.03220.03050.0087-0.0360.2518-0.2985-0.01730.0718-0.01250.20850.1129-0.11170.06260.0013-9.997791.5191219.965
31.5957-0.2529-0.0370.8961-0.19192.96730.0372-0.137-0.09110.0974-0.0036-0.14750.0650.6156-0.0336-0.1440.0873-0.04030.0082-0.0285-0.20725.228574.2339233.297
42.87770.3215-1.32942.35350.54140.0327-0.0478-0.0064-0.1719-0.0713-0.057-0.28370.11880.14680.1048-0.16310.2173-0.01230.1246-0.1129-0.043225.67562.4487222.115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more