[English] 日本語
Yorodumi
- PDB-4crw: Complex of human DDX6 (RECA-C) and CNOT1 (MIF4G) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4crw
TitleComplex of human DDX6 (RECA-C) and CNOT1 (MIF4G)
Components
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
  • PROBABLE ATP-DEPENDENT RNA HELICASE DDX6
KeywordsGENE REGULATION / CCR4-NOT / TRANSLATIONAL REPRESSION / MRNA DECAPPING / DEAD-BOX PROTEIN / P54 / RCK / HELICASE / MRNA SILENCING / MRNA DEADENYLATION / EIF4A / TRANSLATION / MIRNA / P-BODIES
Function / homology
Function and homology information


concave side of sperm head / outer dense fiber / sperm annulus / positive regulation of cytoplasmic mRNA processing body assembly / armadillo repeat domain binding / CCR4-NOT core complex / spermatid differentiation / CCR4-NOT complex / regulation of stem cell population maintenance / mRNA decay by 5' to 3' exoribonuclease ...concave side of sperm head / outer dense fiber / sperm annulus / positive regulation of cytoplasmic mRNA processing body assembly / armadillo repeat domain binding / CCR4-NOT core complex / spermatid differentiation / CCR4-NOT complex / regulation of stem cell population maintenance / mRNA decay by 5' to 3' exoribonuclease / positive regulation of mRNA catabolic process / negative regulation of retinoic acid receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / chromatoid body / miRNA-mediated post-transcriptional gene silencing / trophectodermal cell differentiation / viral RNA genome packaging / Deadenylation of mRNA / miRNA-mediated gene silencing by inhibition of translation / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / RISC complex / peroxisomal membrane / P-body assembly / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / stem cell population maintenance / negative regulation of neuron differentiation / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / heterochromatin / stress granule assembly / nuclear estrogen receptor binding / adherens junction / P-body / helicase activity / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / molecular adaptor activity / RNA helicase activity / negative regulation of translation / RNA helicase / cadherin binding / protein domain specific binding / mRNA binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / extracellular space / RNA binding / ATP binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / 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, 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / Probable ATP-dependent RNA helicase DDX6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChen, Y. / Boland, A. / 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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
B: PROBABLE ATP-DEPENDENT RNA HELICASE DDX6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5549
Polymers47,9092
Non-polymers6457
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.900, 90.840, 95.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 / CNOT1 / CCR4-ASSOCIATED FACTOR 1 / NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 HOMOLOG / NOT1H / HNOT1


Mass: 26783.146 Da / Num. of mol.: 1 / Fragment: CNOT1 MIF4G DOMAIN, RESIDUES 1093-1317
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): ROSETTA2 / References: UniProt: A5YKK6
#2: Protein PROBABLE ATP-DEPENDENT RNA HELICASE DDX6 / DDX6 / ATP-DEPENDENT RNA HELICASE P54 / DEAD BOX PROTEIN 6 / ONCOGENE RCK / ME31B HOMOLOG


Mass: 21126.096 Da / Num. of mol.: 1 / Fragment: DDX6 RECA-C DOMAIN, RESIDUES 307-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: P26196, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG OF CHAIN A. THE FIVE N-TERMINAL RESIDUES ...THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG OF CHAIN A. THE FIVE N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG OF CHAIN B. SEQUENCE NUMBERS ARE SHIFTED BY -11 RESIDUES ACCORDING TO PDB 2WAX AND NCBI GI 458727.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.9 % / Description: NONE
Crystal growpH: 8 / Details: 0.1M TRIS-CL PH=8, 16% PEG6000,, pH 8.0

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 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: 1.75→65.9 Å / Num. obs: 39120 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 24.4 Å2 / Rsym value: 0.05 / Net I/σ(I): 17.1
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.79 / % possible all: 99.5

-
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 ENTRIES 2WAX (CHAIN A), 4GML (CHAIN A)

2wax

4gml


Resolution: 1.75→47.885 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 19.21 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. TLS PARAMETERS WERE REFINED. SIDE CHAINS OF THE FOLLOWING RESIDUES HAVE DOUBLE CONFORMATIONS. CHAIN A, RESIDUES 1127, 1140. CHAIN B, RESIDUES ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. TLS PARAMETERS WERE REFINED. SIDE CHAINS OF THE FOLLOWING RESIDUES HAVE DOUBLE CONFORMATIONS. CHAIN A, RESIDUES 1127, 1140. CHAIN B, RESIDUES 374. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 1087 TO 1091. CHAIN B, RESIDUES 291 TO 295, 454 TO 472.
RfactorNum. reflection% reflection
Rfree0.203 -5 %
Rwork0.1616 --
obs0.1636 39110 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 42 193 3375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113248
X-RAY DIFFRACTIONf_angle_d1.3064376
X-RAY DIFFRACTIONf_dihedral_angle_d14.7461240
X-RAY DIFFRACTIONf_chiral_restr0.051494
X-RAY DIFFRACTIONf_plane_restr0.006554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.26741480.22942590X-RAY DIFFRACTION99
1.7938-1.84230.26481370.21782643X-RAY DIFFRACTION99
1.8423-1.89650.23341360.20052600X-RAY DIFFRACTION99
1.8965-1.95770.22251390.1832624X-RAY DIFFRACTION99
1.9577-2.02770.21991380.172631X-RAY DIFFRACTION99
2.0277-2.10890.1861370.15972645X-RAY DIFFRACTION99
2.1089-2.20480.19071390.14992641X-RAY DIFFRACTION100
2.2048-2.32110.18031390.14892631X-RAY DIFFRACTION100
2.3211-2.46650.19851400.14652655X-RAY DIFFRACTION100
2.4665-2.65690.19551400.1442666X-RAY DIFFRACTION100
2.6569-2.92430.21741410.15332671X-RAY DIFFRACTION99
2.9243-3.34730.17191390.15412678X-RAY DIFFRACTION99
3.3473-4.21690.1841410.14672685X-RAY DIFFRACTION98
4.2169-47.90290.22581440.17922792X-RAY DIFFRACTION97
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)
11.1113-0.0718-0.61950.6329-0.0470.3962-0.11990.3603-0.4644-0.5771-0.02460.2768-0.00990.0865-0.00090.3129-0.00190.00780.2606-0.01560.2937-1.2027-9.8847-10.9956
20.59180.2564-0.29710.3594-0.22210.33730.1920.306-0.0793-0.1012-0.1623-0.41420.1673-0.0193-0.00020.25650.06270.01830.32490.02020.3189.0589-5.1988-8.2976
31.1330.79570.5981.0313-0.07390.8321-0.01360.3289-0.3404-0.4848-0.08960.02510.1824-0.13420.0010.28830.01420.01330.2106-0.03170.2232-2.5645-0.6696-15.4502
40.044-0.03450.14290.3446-0.04660.48090.06350.194-0.17840.0675-0.1301-0.3049-0.02710.19800.1339-0.00020.01090.20540.00470.22294.91135.0915-7.8381
50.57260.00720.64811.3008-0.29640.82460.08670.4396-0.2347-0.4376-0.1950.08710.09210.0371-0.00570.20260.00070.00570.21-0.00810.1549-2.95598.6657-19.6853
60.4845-0.12770.28192.9135-0.39823.617-0.0818-0.0945-0.1220.2097-0.03390.5917-0.1514-0.643-0.00170.22390.02790.03070.2742-0.02920.2734-12.418612.8923-10.4134
70.54310.4677-0.43511.2307-0.06371.71060.08050.2124-0.0142-0.2724-0.06080.0499-0.0678-0.0062-0.00030.1690.00370.00230.1976-0.00220.1713-5.771122.7243-18.5149
80.69270.2622-1.03462.0984-0.54551.8254-0.0379-0.2097-0.04060.22670.03210.1707-0.1514-0.14850.00010.20070.01510.00330.1952-0.00440.1999-9.672121.2875-9.5148
91.237-0.61880.39483.3005-0.38911.8712-0.0479-0.10670.09910.28140.0844-0.0094-0.234-0.06150.00030.24170.01390.00150.1852-00.1607-7.206429.7379-7.6186
101.705-1.2712-0.99412.7374-0.41291.5220.210.31520.0179-0.3072-0.0096-0.0867-0.3312-0.02330.00090.30130.05210.01090.25630.02160.2785-11.588933.0637-17.4297
111.53650.60980.17650.8306-0.52781.5796-0.02670.1672-0.2152-0.11120.03750.07860.2493-0.1049-0.00010.3081-0.0329-0.0050.21650.00080.3109-11.894-16.51010.4279
120.79460.3613-0.17982.035-0.64581.05390.0757-0.1873-0.2758-0.0435-0.1396-0.35670.24770.3837-0.01040.240.0023-0.01220.27730.05410.3032-0.9922-11.79719.6501
131.01920.21090.1621.08940.11490.66280.0688-0.315-0.12530.2359-0.101-0.0813-0.18470.1375-0.00020.2649-0.0609-0.02450.29920.04240.22010.6558-1.658112.9868
141.60831.2499-1.42512.4877-2.41382.38940.1082-0.97720.52551.90320.4280.2269-1.5434-1.08420.16840.784-0.0143-0.00950.64390.0230.3682-8.8583-2.78115.3437
150.75870.1330.59220.13540.09640.46270.0235-0.0763-0.08230.1261-0.0483-0.04760.065-0.17160.00020.229-0.04650.01660.2220.01520.2354-12.8883-12.37668.8938
160.3046-0.07330.10280.1720.04450.1139-0.0992-0.02640.4521-0.0165-0.0588-0.1626-0.2379-0.0520.00060.3258-0.03150.01510.3033-0.01410.3112-16.8493-7.051113.0242
171.82690.1924-0.09810.21070.47011.2233-0.14910.13720.52490.8470.11010.3513-0.8038-0.1698-0.02220.4899-0.0228-0.04350.2340.04590.4335-15.9502-5.48364.0295
181.72550.25660.82031.07590.55521.18420.04070.3281-0.106-0.3213-0.07640.62740.0483-0.3729-0.02650.4031-0.0439-0.02560.35830.02230.377-23.2798-17.24465.8114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1092 THROUGH 1105 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1106 THROUGH 1123 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1124 THROUGH 1142 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1143 THROUGH 1158 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1159 THROUGH 1177 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 1178 THROUGH 1202 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 1203 THROUGH 1228 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 1229 THROUGH 1248 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 1249 THROUGH 1290 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 1291 THROUGH 1317 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 296 THROUGH 320 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 321 THROUGH 358 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 359 THROUGH 379 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 380 THROUGH 391 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 392 THROUGH 403 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 404 THROUGH 414 )
17X-RAY DIFFRACTION17CHAIN B AND (RESID 415 THROUGH 428 )
18X-RAY DIFFRACTION18CHAIN B AND (RESID 429 THROUGH 453 )

+
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