[English] 日本語
Yorodumi
- PDB-7eal: The structure of the A20-Binding Inhibitor of NF-kB 1 in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eal
TitleThe structure of the A20-Binding Inhibitor of NF-kB 1 in complex with di-ubiquitin
Components
  • TNFAIP3-interacting protein 1
  • ubiquitin
KeywordsSIGNALING PROTEIN / M1-ubiquitin / NF-kB / ubiquitin-binding domain
Function / homology
Function and homology information


positive regulation of protein deubiquitination / glycoprotein biosynthetic process / mitogen-activated protein kinase binding / MyD88-dependent toll-like receptor signaling pathway / leukocyte cell-cell adhesion / negative regulation of viral genome replication / negative regulation of canonical NF-kappaB signal transduction / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) ...positive regulation of protein deubiquitination / glycoprotein biosynthetic process / mitogen-activated protein kinase binding / MyD88-dependent toll-like receptor signaling pathway / leukocyte cell-cell adhesion / negative regulation of viral genome replication / negative regulation of canonical NF-kappaB signal transduction / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Defective CFTR causes cystic fibrosis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Stabilization of p53 / EGFR downregulation
Similarity search - Function
Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / TNFAIP3-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLo, Y.C. / Lin, S.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 107-2320-B-006 -062 -MY3 Taiwan
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural and Biochemical Basis for Higher-Order Assembly between A20-Binding Inhibitor of NF-kappa B 1 (ABIN1) and M1-Linked Ubiquitins.
Authors: Hong, J.Y. / Lin, S.C. / Kuo, B.J. / Lo, Y.C.
History
DepositionMar 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: ubiquitin
B: TNFAIP3-interacting protein 1
C: TNFAIP3-interacting protein 1
D: ubiquitin
E: TNFAIP3-interacting protein 1
F: TNFAIP3-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2937
Polymers85,2016
Non-polymers921
Water19811
1
A: ubiquitin
B: TNFAIP3-interacting protein 1
C: TNFAIP3-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)42,6003
Polymers42,6003
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-35 kcal/mol
Surface area16100 Å2
MethodPISA
2
D: ubiquitin
E: TNFAIP3-interacting protein 1
F: TNFAIP3-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6924
Polymers42,6003
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-39 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.753, 59.990, 84.058
Angle α, β, γ (deg.)90.00, 109.71, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ubiquitin / diubiquitin


Mass: 17135.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein
TNFAIP3-interacting protein 1 / A20-binding inhibitor of NF-kappa-B activation 1 / ABIN-1 / HIV-1 Nef-interacting protein / Nef- ...A20-binding inhibitor of NF-kappa-B activation 1 / ABIN-1 / HIV-1 Nef-interacting protein / Nef-associated factor 1 / Naf1 / Nip40-1 / Virion-associated nuclear shuttling protein / VAN / hVAN


Mass: 12732.300 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNIP1, KIAA0113, NAF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15025
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.33 % / Description: needle shape
Crystal growTemperature: 255 K / Method: vapor diffusion / Details: 0.1M Citrate pH 5.5, 10% Iso-propanol, 20% PEG 400

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 26579 / % possible obs: 97.94 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.029 / Net I/σ(I): 16.05
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.04 / Num. unique obs: 2342 / Χ2: 1.001 / % possible all: 87.13

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H07

5h07


Resolution: 2.5→23.563 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 1301 4.9 %
Rwork0.1839 --
obs0.1859 26576 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→23.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 6 11 4579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094601
X-RAY DIFFRACTIONf_angle_d0.9976149
X-RAY DIFFRACTIONf_dihedral_angle_d8.1772936
X-RAY DIFFRACTIONf_chiral_restr0.047705
X-RAY DIFFRACTIONf_plane_restr0.006805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.57910.29181390.23592495X-RAY DIFFRACTION88
2.5791-2.69630.26711660.22442801X-RAY DIFFRACTION100
2.6963-2.83820.29051330.20622844X-RAY DIFFRACTION100
2.8382-3.01570.24481350.20352870X-RAY DIFFRACTION100
3.0157-3.2480.24661480.19882856X-RAY DIFFRACTION100
3.248-3.57390.25621290.18232858X-RAY DIFFRACTION100
3.5739-4.08870.19421400.16042864X-RAY DIFFRACTION100
4.0887-5.14250.18321700.15562831X-RAY DIFFRACTION99
5.1425-100.22841410.19572856X-RAY DIFFRACTION96
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)
12.9529-0.24181.84925.5481-0.77041.2349-0.417-0.4672-1.0953-0.3013-0.1296-1.24021.76720.76760.20070.59060.32240.03430.89960.24990.6571176.658310.437737.3774
29.6542.9065-0.28312.56622.0185.7471-0.05240.0358-1.0823-0.09490.1945-0.24860.8460.4721-0.24250.42780.10350.05070.39310.05520.5082167.68812.279732.8636
33.44371.7152-3.23492.4699-2.7313.84770.1758-0.41840.88740.0613-0.44160.5762-1.90430.31130.09680.63650.0646-0.06580.7532-0.02410.4498173.426223.058535.9884
45.19471.11-0.74123.78890.1211.8289-0.372-0.6582-0.62390.19740.0527-0.6249-0.09121.04940.31430.34740.01220.0130.70630.12710.3277171.485916.954637.7658
52.33531.8166-1.47052.6794-2.72417.7630.2312-0.74760.9417-0.4453-0.14411.43470.5285-0.6186-0.06160.204-0.01730.01980.3269-0.01510.4087141.81865.13629.1077
66.633-2.6965-4.87972.77331.56343.8432-0.11090.8497-0.0521-0.5166-0.0897-0.3402-0.1253-0.29840.11070.3658-0.01720.03970.3160.02210.3142152.67039.403827.0106
73.68841.32691.5664.1644-2.84353.89960.00410.2871-0.85360.61210.1566-0.81670.12580.00570.15510.44440.0533-0.00850.3543-0.00460.4981153.45921.083628.1405
87.7515-1.0314-0.83558.2737-2.69836.327-0.21580.864-0.1316-1.5777-0.0021-0.00520.8289-0.07630.08830.5821-0.00650.00840.3018-0.08120.3094148.734-0.546919.5182
94.6832-4.349-3.62127.2015.23043.86670.27720.86631.1041-1.44380.0824-0.5357-0.5811-0.2799-0.18970.71190.01180.09420.32740.09390.3286149.667512.704718.9961
108.7641-1.521-1.62113.37933.91154.5168-0.04560.5052-0.3521-0.8905-0.42110.03640.32420.31460.61560.62750.04450.05920.33760.01530.2648144.9277-4.435221.3778
111.87681.10612.12230.64930.92354.072-0.1562-0.21080.16210.056-0.08480.1885-0.0995-0.2770.19150.37410.05720.04550.27430.01610.3291139.61521.612934.512
123.5665-1.14151.55851.1093-0.30642.3236-0.0521-0.0742-0.5049-0.00560.16480.2597-0.2776-0.3564-0.17110.3796-0.01770.06910.30570.03890.3991137.61117.176334.2095
137.97050.78451.25927.20583.24146.9509-0.0762-0.44170.9622-0.01290.16340.311-0.88170.4608-0.18780.4433-0.03380.05370.27510.01260.2708156.0345-22.419828.2013
147.3017-2.51341.27222.1391-0.59652.48220.1185-0.00380.1784-0.5831-0.18221.0659-1.063-0.7694-0.08140.49220.0590.1430.3630.10020.3752150.0718-23.067521.0601
154.0709-0.27711.20447.0443-4.50036.88320.0020.1168-0.2105-0.17430.2081-0.02450.1316-0.0757-0.17290.23150.01280.07830.22970.00630.2436156.1788-31.009924.2788
160.426-0.09090.86161.3509-0.77077.98940.0793-0.15-0.04620.1310.18830.2475-0.0690.1255-0.25880.30960.00510.10.3628-0.04870.3362159.7787-26.166215.4959
174.4214-3.72353.24729.3958-2.96182.6441-0.0184-0.1655-0.1413-0.1861-0.17050.31640.47370.67240.1190.2084-0.05840.01170.3098-0.0250.2522149.617-18.09250.27
185.32043.90952.35074.02-1.03068.44850.11830.04530.0490.2104-0.04950.1999-0.2106-0.0854-0.00770.23910.01380.05710.35150.01370.3045148.1746-8.92614.1287
197.31730.35132.66033.72743.55884.159-0.1965-0.0905-0.4884-0.20040.07451.61110.188-1.62150.25660.4902-0.1086-0.00650.54160.04370.5743136.5489-13.6231.3609
206.1615-2.4984-1.58572.1349-1.71927.82510.17390.0196-0.15420.32330.41230.96840.6049-0.8331-0.34640.3191-0.1478-0.02180.40610.0020.6627140.5763-22.89681.9749
218.3397-1.43720.40753.3396-4.03717.83630.3025-0.16391.14410.1327-0.50111.0811-0.8186-0.86310.29680.35610.09470.04610.44680.02580.4823143.9344-5.6626-2.3693
226.1908-1.43255.14520.8955-2.12095.56660.19650.2354-0.2602-0.29770.00420.16230.1756-0.1052-0.17650.3630.0129-0.00340.3794-0.0650.3149154.7213-30.7426-5.478
233.04510.02532.28180.85970.34672.6913-0.03740.34680.0849-0.183-0.11510.0584-0.18640.16640.21050.33190.01310.03980.5075-0.02250.3414157.9344-26.4318-4.3113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 56 )
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 122 )
7X-RAY DIFFRACTION7chain 'A' and (resid 123 through 134 )
8X-RAY DIFFRACTION8chain 'A' and (resid 135 through 154 )
9X-RAY DIFFRACTION9chain 'A' and (resid 155 through 165 )
10X-RAY DIFFRACTION10chain 'A' and (resid 166 through 176 )
11X-RAY DIFFRACTION11chain 'B' and (resid 452 through 513 )
12X-RAY DIFFRACTION12chain 'C' and (resid 453 through 513 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 22 )
14X-RAY DIFFRACTION14chain 'D' and (resid 23 through 34 )
15X-RAY DIFFRACTION15chain 'D' and (resid 35 through 65 )
16X-RAY DIFFRACTION16chain 'D' and (resid 66 through 76 )
17X-RAY DIFFRACTION17chain 'D' and (resid 101 through 122 )
18X-RAY DIFFRACTION18chain 'D' and (resid 123 through 144 )
19X-RAY DIFFRACTION19chain 'D' and (resid 145 through 154 )
20X-RAY DIFFRACTION20chain 'D' and (resid 155 through 165 )
21X-RAY DIFFRACTION21chain 'D' and (resid 166 through 176 )
22X-RAY DIFFRACTION22chain 'E' and (resid 449 through 513 )
23X-RAY DIFFRACTION23chain 'F' and (resid 446 through 511 )

+
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://pdbjlvh1.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