[English] 日本語
Yorodumi
- PDB-8z36: Crystal structure of HOIP PUB domain in complex with sertraline c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8z36
TitleCrystal structure of HOIP PUB domain in complex with sertraline complex
ComponentsE3 ubiquitin-protein ligase RNF31
KeywordsLIGASE / E3 ubiquitin-protein ligase HOIP / sertraline
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / ubiquitin protein ligase binding / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : / HOIP UBA domain pair ...E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / PUB domain / PUB-like domain superfamily / PUB domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-SRE / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsZhong, F. / Ruan, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22377119 China
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Repurposing Tolfenamic Acid to Anchor the Uncharacterized Pocket of the PUB Domain for Proteolysis of the Atypical E3 Ligase HOIP.
Authors: Zhong, F. / Zhou, Y. / Liu, M. / Wang, L. / Li, F. / Zhang, J. / Han, Z. / Shi, Y. / Gao, J. / Ruan, K.
History
DepositionApr 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31
C: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1426
Polymers60,2243
Non-polymers9193
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.173, 114.806, 66.130
Angle α, β, γ (deg.)90.00, 110.52, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase RNF31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 20074.553 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Escherichia coli (E. coli)
References: UniProt: Q96EP0, RBR-type E3 ubiquitin transferase
#2: Chemical ChemComp-SRE / (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine / Sertraline


Mass: 306.230 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H17Cl2N / Feature type: SUBJECT OF INVESTIGATION / Comment: antidepressant, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 20 mM Na3PO4, 20 mM K3PO4, pH 7.5, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.63→42.1 Å / Num. obs: 18841 / % possible obs: 98.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.5
Reflection shellResolution: 2.63→2.75 Å / Rmerge(I) obs: 0.493 / Num. unique obs: 2295

-
Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→34.53 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 1884 10.01 %
Rwork0.2202 --
obs0.2252 18830 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 20 58 4126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024149
X-RAY DIFFRACTIONf_angle_d0.4885659
X-RAY DIFFRACTIONf_dihedral_angle_d4.992585
X-RAY DIFFRACTIONf_chiral_restr0.036649
X-RAY DIFFRACTIONf_plane_restr0.004747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.70.34651420.27361277X-RAY DIFFRACTION98
2.7-2.780.34331440.2611301X-RAY DIFFRACTION98
2.78-2.870.32311450.27031306X-RAY DIFFRACTION98
2.87-2.970.32251460.26951299X-RAY DIFFRACTION98
2.97-3.090.32621430.26191294X-RAY DIFFRACTION98
3.09-3.230.32111450.2411309X-RAY DIFFRACTION99
3.23-3.40.29351440.2521289X-RAY DIFFRACTION98
3.4-3.620.30441450.24221307X-RAY DIFFRACTION99
3.62-3.890.22531470.21311323X-RAY DIFFRACTION98
3.89-4.290.25131430.19131284X-RAY DIFFRACTION98
4.29-4.90.20241470.17181324X-RAY DIFFRACTION98
4.9-6.170.27671460.23721321X-RAY DIFFRACTION99
6.18-34.530.24231470.18921312X-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)
10.42150.0771-0.51190.3751-0.15640.4761-0.2497-0.25350.7692-0.21080.0630.0961-0.8897-0.4315-00.57380.1479-0.08430.3948-0.00540.5017-34.30326.926117.4891
21.0190.1601-0.39610.7707-0.60991.01520.0264-0.0948-0.0553-0.1033-0.0853-0.09590.0528-0.0291-00.208-0.0046-0.01720.16770.02730.2023-24.22510.920715.3242
30.18350.40060.02891.3228-0.31350.68770.053-0.08290.1352-0.2305-0.17510.0647-0.1486-0.0537-0.00080.23710.0267-0.01060.2230.01020.2737-28.681414.940914.4468
40.4464-0.1808-0.48190.4479-0.060.37720.20050.2845-0.3583-0.17130.1398-0.21160.13090.33730.00120.310.066-0.05510.2468-0.13980.3015-24.4191-19.1939-8.274
50.5158-0.1152-0.31340.44640.07150.71220.2191-0.16640.02250.09820.2242-0.0152-0.1409-0.06360.19680.1808-0.0315-0.00880.322-0.06280.2452-34.5857-7.3059-0.4979
60.1611-0.03360.12420.0013-0.00240.09720.47210.45850.6958-0.4613-0.0279-0.3492-0.3071-0.3775-0.00760.68630.10020.1290.40860.1550.3754-38.58562.1011-15.7429
71.2278-1.24950.1951.18210.35531.1418-0.05070.19630.0805-0.11540.3624-0.2433-0.14460.0580.02110.274-0.03940.0130.2765-0.05070.2992-31.7072-5.681-4.5159
80.46910.91760.63642.1191.28221.1202-0.1523-1.39790.03630.0259-1.0840.97740.3046-0.6465-0.88290.2319-0.36310.37380.89530.20180.2859-32.2577-9.542146.3154
90.2686-0.3807-0.18631.76670.21490.2036-0.2328-0.56810.43650.61290.2479-0.6565-0.2683-0.10610.04540.1916-0.072-0.07030.40760.11340.2825-17.5606-3.521636.8988
100.6876-0.17850.03940.0274-0.10220.6598-0.3366-0.24690.1599-0.45410.23780.32020.0069-0.3276-0.00450.3162-0.0941-0.00870.28420.08290.2094-30.9575-9.288828.5112
110.35320.0023-0.09990.1640.19330.19940.1134-0.64120.3989-0.5571-0.53850.172-0.23960.3149-0.00470.3894-0.0262-0.030.29020.01430.2621-24.3662-7.734520.3089
120.1079-0.0492-0.03030.0246-0.0280.0754-0.23080.0404-0.24330.008-0.0282-0.02820.65840.21190.00030.51410.10650.06370.33720.06220.4467-21.0582-16.730124.5254
130.01090.026-0.01140.0535-0.01080.0172-0.07030.0692-0.45560.36140.05160.10730.1710.12830.00061.2709-0.06510.05480.49140.11950.7161-26.9809-26.655928.8253
140.18270.27090.23320.21270.13770.1-0.0145-0.683-0.0808-0.31420.05310.31070.1882-0.17360.00420.3698-0.10990.02590.48450.09310.2909-28.0989-7.067438.4798
151.0318-0.0823-0.20670.184-0.00510.2710.1992-0.14080.6361-0.0032-0.0060.1059-0.0812-0.22770.01410.4422-0.11190.03360.7959-0.23350.4019-22.8478.117843.8459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 178 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 43 )
5X-RAY DIFFRACTION5chain 'B' and (resid 44 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 107 )
7X-RAY DIFFRACTION7chain 'B' and (resid 108 through 179 )
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 43 )
9X-RAY DIFFRACTION9chain 'C' and (resid 44 through 64 )
10X-RAY DIFFRACTION10chain 'C' and (resid 65 through 96 )
11X-RAY DIFFRACTION11chain 'C' and (resid 97 through 114 )
12X-RAY DIFFRACTION12chain 'C' and (resid 115 through 133 )
13X-RAY DIFFRACTION13chain 'C' and (resid 134 through 142 )
14X-RAY DIFFRACTION14chain 'C' and (resid 143 through 164 )
15X-RAY DIFFRACTION15chain 'C' and (resid 165 through 179 )

+
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