[English] 日本語
Yorodumi
- PDB-7yui: Crystal structure of HOIL-1L(195-423) in complex with the linear ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yui
TitleCrystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin
Components
  • Polyubiquitin-C
  • RanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsPROTEIN BINDING / E3 / ubiquitination
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity / Maturation of protein E ...protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity / 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 / protein sequestering activity / 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 / ubiquitin binding / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / 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 / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Degradation of GLI1 by the proteasome / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR2 signaling / Hedgehog ligand biogenesis
Similarity search - Function
: / : / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. ...: / : / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsXiao, L. / Pan, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21621002 China
CitationJournal: Sci Adv / Year: 2023
Title: Mechanistic insights into the enzymatic activity of E3 ligase HOIL-1L and its regulation by the linear ubiquitin chain binding.
Authors: Xu, X. / Wang, Y. / Zhang, Y. / Wang, Y. / Yin, Y. / Peng, C. / Gong, X. / Li, M. / Zhang, Y. / Zhang, M. / Tang, Y. / Zhou, X. / Liu, H. / Pan, L.
History
DepositionAug 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author / Item: _audit_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyubiquitin-C
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7257
Polymers61,3982
Non-polymers3275
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-32 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.500, 90.304, 117.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Polyubiquitin-C


Mass: 34551.590 Da / Num. of mol.: 1
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 RanBP-type and C3HC4-type zinc finger-containing protein 1


Mass: 26846.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBCK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BYM8, RBR-type E3 ubiquitin transferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium chloride, 0.1 M Tris(pH 8), 20 %(w/v)PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL17B / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.599→71.59 Å / Num. obs: 19702 / % possible obs: 99.5 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 13.7
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 1.151 / Num. unique obs: 929

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R71, 3B08

7r71

3b08


Resolution: 2.599→71.587 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2575 942 4.78 %
Rwork0.2026 18748 -
obs0.2052 19690 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.64 Å2 / Biso mean: 57.7576 Å2 / Biso min: 22.12 Å2
Refinement stepCycle: final / Resolution: 2.599→71.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4267 0 5 74 4346
Biso mean--51.31 46.65 -
Num. residues----537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.599-2.73570.36051380.2948257097
2.7357-2.90710.34951440.26482634100
2.9071-3.13160.33121230.25452645100
3.1316-3.44670.29361520.23492656100
3.4467-3.94550.26691280.18932682100
3.9455-4.97070.19471260.16692720100
4.9707-71.5870.21031310.1769284199
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)
13.5009-0.6974-0.48291.711-0.08642.1060.1723-0.1681-0.0503-0.1285-0.06740.1777-0.0605-0.0911-0.06750.28630.018-0.01290.3032-00.2142-27.756214.9979-2.035
23.8342-0.0218-1.49170.6116-0.08211.7761-0.08690.1188-0.2895-0.0655-0.0769-0.11750.18620.05650.10590.34470.0086-0.00860.2781-0.00750.2824-6.617312.7325-16.149
32.317-0.859-1.80461.07550.76432.8698-0.08690.23620.1349-0.0735-0.19680.5879-0.1221-0.81820.23350.51570.14530.040.5838-0.06480.697516.76085.5905-47.6788
43.1992-0.5638-0.03571.97970.45882.43740.12520.49580.7867-0.2466-0.08450.1174-0.4939-0.212-0.11790.50170.04530.0210.40690.11860.65142.763214.8549-62.6222
56.45180.7419-1.38983.7641-0.21834.4790.4840.97670.4567-0.6437-0.05540.13310.075-0.0597-0.29790.36290.10980.00020.47720.02340.2752-19.967321.367-22.9291
63.5966-2.4398-4.01334.1413.00924.46230.43680.33380.7614-0.4982-0.0421-0.4527-0.2668-0.0823-0.34970.408-0.02460.02510.39530.02850.40979.503620.5349-29.9803
73.75030.2159-1.39522.5962-0.53395.05150.0306-0.42720.03110.53370.07870.0675-0.13880.1482-0.03390.4107-0.0280.09940.4271-0.08510.362931.9452-4.2218-38.2002
83.94630.9318-2.06490.7975-0.27862.59240.1208-0.00360.2804-0.00530.01430.1311-0.08590.0559-0.11880.33610.00630.00070.23430.00130.389545.8791-0.4042-58.6577
98.4214-6.6287-1.81976.67251.77675.42030.49340.393-0.011-0.5333-0.4116-0.4362-0.05190.5918-0.12650.3630.004-0.00540.45130.08570.430969.4131-2.4271-80.8469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 54 )A0 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 153 )A55 - 153
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 234 )A154 - 234
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 304 )A235 - 304
5X-RAY DIFFRACTION5chain 'B' and (resid 193 through 233 )B193 - 233
6X-RAY DIFFRACTION6chain 'B' and (resid 234 through 270 )B234 - 270
7X-RAY DIFFRACTION7chain 'B' and (resid 271 through 300 )B271 - 300
8X-RAY DIFFRACTION8chain 'B' and (resid 301 through 399 )B301 - 399
9X-RAY DIFFRACTION9chain 'B' and (resid 400 through 424 )B400 - 424

+
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