[English] 日本語
Yorodumi
- PDB-5h7s: Structural basis of the flanking zinc-finger motifs crucial for t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h7s
TitleStructural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain
Components
  • E3 ubiquitin-protein ligase LNX
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin-like 1
KeywordsPROTEIN BINDING/LIGASE/TRANSFERASE / RING / ubiquitin / E3 ligase / zinc finger motif / PROTEIN BINDING-LIGASE-TRANSFERASE complex
Function / homology
Function and homology information


UBC13-MMS2 complex / synapse maturation / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / symbiont entry into host cell via disruption of host cell glycocalyx / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair ...UBC13-MMS2 complex / synapse maturation / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / symbiont entry into host cell via disruption of host cell glycocalyx / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / regulation of DNA repair / TICAM1, RIP1-mediated IKK complex recruitment / negative regulation of TORC1 signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / antiviral innate immune response / activated TAK1 mediates p38 MAPK activation / positive regulation of DNA repair / hippocampal mossy fiber to CA3 synapse / ubiquitin binding / NOD1/2 Signaling Pathway / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / PDZ domain binding / Nonhomologous End-Joining (NHEJ) / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / Formation of Incision Complex in GG-NER / positive regulation of NF-kappaB transcription factor activity / FCERI mediated NF-kB activation / G2/M DNA damage checkpoint / RING-type E3 ubiquitin transferase / Interleukin-1 signaling / Aggrephagy / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / T cell receptor signaling pathway / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / postsynapse / protein ubiquitination / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Zinc finger, C3HC4 type (RING finger) / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Zinc finger, C3HC4 type (RING finger) / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PDZ domain / Ring finger / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tail fiber / Ubiquitin-conjugating enzyme E2 N / E3 ubiquitin-protein ligase LNX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsNayak, D. / Sivaraman, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore)R154000625112 Singapore
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structure of LNX1:Ubc13~Ubiquitin Complex Reveals the Role of Additional Motifs for the E3 Ligase Activity of LNX1.
Authors: Nayak, D. / Sivaraman, J.
History
DepositionNov 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Ubiquitin-like 1
D: E3 ubiquitin-protein ligase LNX
A: Ubiquitin-conjugating enzyme E2 N
F: Ubiquitin-like 1
B: E3 ubiquitin-protein ligase LNX
C: Ubiquitin-conjugating enzyme E2 N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,18014
Polymers80,6576
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-21 kcal/mol
Surface area32710 Å2
Unit cell
Length a, b, c (Å)122.372, 122.372, 135.199
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21B
12E
22F
13A
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLYGLYDB2 - 1252 - 125
21PROPROGLYGLYBE2 - 1252 - 125
12METMETGLYGLYEA1 - 761 - 76
22METMETGLYGLYFD1 - 761 - 76
13LEULEUASNASNAC4 - 1514 - 151
23LEULEUASNASNCF4 - 1514 - 151

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Ubiquitin-like 1


Mass: 8576.831 Da / Num. of mol.: 2
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
#2: Protein E3 ubiquitin-protein ligase LNX / Ligand of Numb-protein X 1 / Numb-binding protein 1 / PDZ domain-containing RING finger protein 2 / ...Ligand of Numb-protein X 1 / Numb-binding protein 1 / PDZ domain-containing RING finger protein 2 / RING-type E3 ubiquitin transferase LNX


Mass: 14625.937 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 11-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LNX1, LNX, PDZRN2, UNQ574/PRO1136 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TBB1, RING-type E3 ubiquitin transferase
#3: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17125.705 Da / Num. of mol.: 2 / Mutation: C87K, K92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.04 M Citric acid, 0.06 M BIS-TRIS propane, pH 6.4, 20% w/v polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.48→134.95 Å / Num. obs: 15353 / % possible obs: 99.8 % / Redundancy: 9.9 % / Net I/σ(I): 16.1
Reflection shellResolution: 3.48→3.81 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0171refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DIN, 3HCT, 1UBQ

5din

3hct

1ubq


Resolution: 3.49→105.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 108.669 / SU ML: 0.63 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28649 1421 10 %RANDOM
Rwork0.24085 ---
obs0.24547 12753 92.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.12 Å2-0 Å2
2---0.23 Å20 Å2
3---0.75 Å2
Refinement stepCycle: 1 / Resolution: 3.49→105.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 8 0 5534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195668
X-RAY DIFFRACTIONr_bond_other_d0.0020.025326
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9837704
X-RAY DIFFRACTIONr_angle_other_deg0.9863.00312400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.95690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34124.688256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.527151006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5041532
X-RAY DIFFRACTIONr_chiral_restr0.0820.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216152
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021048
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D75780.05
12B75780.05
21E43720.01
22F43720.01
31A94240.05
32C94240.05
LS refinement shellResolution: 3.486→3.576 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.632 61 -
Rwork0.641 535 -
obs--53.17 %
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)
14.35692.16360.8396.0355-0.10035.4240.2374-0.06260.04750.0781-0.03830.89910.3108-0.8713-0.19910.3143-0.0203-0.01150.29140.02090.157741.4-18.3618
211.5085-0.57421.23748.5018-2.85976.814-0.4070.19360.71290.29590.1033-0.6606-0.36140.43590.30380.60350.00920.050.6401-0.17520.528168.318-14.39133.483
36.39771.69492.4644.62723.1739.4384-0.23650.44380.0255-0.35940.24890.87060.25840.125-0.01250.4704-0.0147-0.01090.16210.17630.384955.448-16.238-23.898
47.6013-0.5402-0.46381.9862-0.71153.71250.2219-0.14420.2773-0.0613-0.0795-0.5624-0.29370.837-0.14230.4439-0.07220.0740.1926-0.05810.195366.168-9.2736.861
56.5685-3.85454.28072.6802-1.87143.87750.22870.23570.1078-0.2235-0.50190.07630.172-0.15020.27321.3254-0.2505-0.01921.49010.12440.961641.544-21.336-9.27
68.49231.09314.48893.4783-2.08979.40460.0567-0.9482-0.01930.50390.0858-0.20140.057-0.5292-0.14240.53160.15160.09350.2472-0.09370.22654.232-19.06848.542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D2 - 125
2X-RAY DIFFRACTION1D201
3X-RAY DIFFRACTION1D202
4X-RAY DIFFRACTION1D204
5X-RAY DIFFRACTION2E1 - 76
6X-RAY DIFFRACTION3A4 - 151
7X-RAY DIFFRACTION4B2 - 125
8X-RAY DIFFRACTION4B201
9X-RAY DIFFRACTION4B202
10X-RAY DIFFRACTION4B204
11X-RAY DIFFRACTION5F1 - 76
12X-RAY DIFFRACTION6C4 - 151

+
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