[English] 日本語
Yorodumi
- PDB-6a6i: Crystal structure of the winged-helix domain of Cockayne syndrome... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a6i
TitleCrystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin
Components
  • (Polyubiquitin- ...) x 2
  • Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant
KeywordsHYDROLASE / DNA repair / helicase / ubiquitin / molecular signaling
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of proteasomal protein catabolic process ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Termination of translesion DNA synthesis / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling
Similarity search - Function
SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain ...SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / helicase superfamily c-terminal domain / Ubiquitin domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Polyubiquitin-B / Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTakahashi, T.S. / Sato, Y. / Fukai, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H04750 Japan
Japan Society for the Promotion of Science15F15386 Japan
Japan Science and TechnologyJPMJCR1XMX5 Japan
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis of ubiquitin recognition by the winged-helix domain of Cockayne syndrome group B protein.
Authors: Takahashi, T.S. / Sato, Y. / Yamagata, A. / Goto-Ito, S. / Saijo, M. / Fukai, S.
History
DepositionJun 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant
B: Polyubiquitin-B
C: Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant
D: Polyubiquitin-B
E: Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant
F: Polyubiquitin-B
G: Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant
H: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,31512
Polymers79,0038
Non-polymers3124
Water1,892105
1
A: Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7993
Polymers19,7072
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-7 kcal/mol
Surface area9620 Å2
MethodPISA
2
C: Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8354
Polymers19,7072
Non-polymers1282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-5 kcal/mol
Surface area9790 Å2
MethodPISA
3
E: Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant
F: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)19,7942
Polymers19,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-6 kcal/mol
Surface area9460 Å2
MethodPISA
4
G: Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant
H: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8863
Polymers19,7942
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-10 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.161, 101.705, 66.008
Angle α, β, γ (deg.)90.00, 101.81, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ACEG

#1: Protein
Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant


Mass: 11102.466 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59FF6

-
Polyubiquitin- ... , 2 types, 4 molecules BDFH

#2: Protein Polyubiquitin-B


Mass: 8604.845 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76 / Mutation: K48R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Protein Polyubiquitin-B


Mass: 8691.918 Da / Num. of mol.: 2 / Fragment: UNP residues 1-77 / Mutation: M77D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

-
Non-polymers , 3 types, 109 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 21604 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rpim(I) all: 0.094 / Rsym value: 0.21 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1229 / CC1/2: 0.599 / Rsym value: 0.583 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 2.6→39.96 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.05
RfactorNum. reflection% reflection
Rfree0.2358 1099 5.15 %
Rwork0.1785 --
obs0.1814 21345 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5282 0 19 105 5406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025378
X-RAY DIFFRACTIONf_angle_d0.6777235
X-RAY DIFFRACTIONf_dihedral_angle_d11.452069
X-RAY DIFFRACTIONf_chiral_restr0.027824
X-RAY DIFFRACTIONf_plane_restr0.002939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.71830.29111020.24192328X-RAY DIFFRACTION92
2.7183-2.86160.30741500.23152557X-RAY DIFFRACTION100
2.8616-3.04080.29781680.21812508X-RAY DIFFRACTION100
3.0408-3.27550.25541480.19752547X-RAY DIFFRACTION100
3.2755-3.60490.2241160.17852573X-RAY DIFFRACTION100
3.6049-4.12610.19681400.1522558X-RAY DIFFRACTION100
4.1261-5.19670.20721270.14472578X-RAY DIFFRACTION100
5.1967-39.96470.22121480.17622597X-RAY DIFFRACTION100
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)
12.20861.0056-0.22822.94320.82533.29460.0181-0.1615-0.13760.1057-0.1174-0.26080.22860.23860.09230.29390.0024-0.01040.25770.03730.308525.31851.706731.282
23.36960.27990.77112.4334-1.32964.37080.0745-0.0638-0.051-0.1467-0.00180.05570.2492-0.3613-0.08680.2138-0.00990.00480.2517-0.03460.23325.4694-1.146220.7303
32.9038-1.0074-0.25543.3034-0.68942.3995-0.01-0.33680.01280.39420.02020.055-0.21670.0641-0.02810.3223-0.0406-0.01310.2558-0.02560.2625.663822.418434.853
43.81781.70810.77392.5179-0.46182.6514-0.08990.30290.0921-0.0020.03520.09350.0663-0.13550.03640.24780.02760.02220.20380.00030.235818.335530.528114.8865
52.52070.42911.34932.84141.98864.354-0.0214-0.0611-0.03690.1283-0.08120.15070.11870.05540.04760.28190.02260.01670.26320.01670.313436.88140.26425.4328
64.0099-0.0063-1.28613.97920.76912.45990.08320.15870.3713-0.07970.0602-0.081-0.3087-0.0089-0.14120.2624-0.03040.00480.26140.02610.289748.938319.90796.3685
73.39130.03380.58033.1936-0.17422.31540.0961-0.08190.2057-0.368-0.09560.057-0.4747-0.0473-0.10560.4030.00320.04370.4354-0.01670.2939-1.26724.073246.6542
83.8435-0.6716-1.10473.9870.28014.4388-0.17280.3535-0.44790.13060.04520.14720.2318-0.03120.1240.3094-0.00660.030.4203-0.06460.4029-3.30543.589454.3669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1400 through 1493)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 74)
3X-RAY DIFFRACTION3(chain 'C' and resid 1400 through 1493)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 76)
5X-RAY DIFFRACTION5(chain 'E' and resid 1400 through 1493)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 74)
7X-RAY DIFFRACTION7(chain 'G' and resid 1414 through 1493)
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 74)

+
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