[English] 日本語
Yorodumi
- PDB-7nzd: Fourth SH3 domain of POSH (Plenty of SH3 Domains protein) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nzd
TitleFourth SH3 domain of POSH (Plenty of SH3 Domains protein)
ComponentsE3 ubiquitin-protein ligase SH3RF1
KeywordsSIGNALING PROTEIN / MAP-kinase scaffold activity ubiquitin protein ligase activity
Function / homology
Function and homology information


regulation of CD4-positive, alpha-beta T cell differentiation / regulation of CD8-positive, alpha-beta T cell proliferation / MAP-kinase scaffold activity / RHOV GTPase cycle / response to aldosterone / protein autoubiquitination / : / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / neuron migration ...regulation of CD4-positive, alpha-beta T cell differentiation / regulation of CD8-positive, alpha-beta T cell proliferation / MAP-kinase scaffold activity / RHOV GTPase cycle / response to aldosterone / protein autoubiquitination / : / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / neuron migration / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / lamellipodium / protein ubiquitination / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / metal ion binding / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase SH3RF1, second SH3 domain / SH3RF1/SH3RF3, fourth SH3 domain / : / Zinc finger, C3HC4 type (RING finger) / Variant SH3 domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / SH3 domain / Zinc finger RING-type profile. ...E3 ubiquitin-protein ligase SH3RF1, second SH3 domain / SH3RF1/SH3RF3, fourth SH3 domain / : / Zinc finger, C3HC4 type (RING finger) / Variant SH3 domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / SH3 domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / E3 ubiquitin-protein ligase SH3RF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPalencia, A. / Bessa, L.M. / Jensen, M.R.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)NovoTarget- RC18114CC France
Agence Nationale de la Recherche (ANR)MAPKassembly France
CitationJournal: Nature / Year: 2022
Title: Visualizing protein breathing motions associated with aromatic ring flipping.
Authors: Marino Perez, L. / Ielasi, F.S. / Bessa, L.M. / Maurin, D. / Kragelj, J. / Blackledge, M. / Salvi, N. / Bouvignies, G. / Palencia, A. / Jensen, M.R.
History
DepositionMar 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: E3 ubiquitin-protein ligase SH3RF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4083
Polymers7,2401
Non-polymers1682
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, chain A is a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint4 kcal/mol
Surface area4460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.520, 45.520, 65.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11AAA-902-

PEG

21AAA-1087-

HOH

31AAA-1088-

HOH

-
Components

#1: Protein E3 ubiquitin-protein ligase SH3RF1 / Plenty of SH3s / Protein POSH / RING finger protein 142 / RING-type E3 ubiquitin transferase SH3RF1 ...Plenty of SH3s / Protein POSH / RING finger protein 142 / RING-type E3 ubiquitin transferase SH3RF1 / SH3 domain-containing RING finger protein 1 / SH3 multiple domains protein 2


Mass: 7240.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GRR belongs to expression vector pESPRIT / Source: (gene. exp.) Homo sapiens (human) / Gene: SH3RF1, KIAA1494, POSH, POSH1, RNF142, SH3MD2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7Z6J0, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.6 Å3/Da / Density % sol: 53 % / Description: 3D large crystal
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1M MES pH 6.5, 23% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2020
RadiationMonochromator: MIRROS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.45→65.74 Å / Num. obs: 14475 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 1 / Net I/σ(I): 23.8
Reflection shellResolution: 1.45→1.48 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 703 / CC1/2: 0.52 / % possible all: 99.29

-
Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model build with the template 2LJ1

2lj1


Resolution: 1.45→65.74 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.052 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2275 716 4.957 %
Rwork0.1601 13727 -
all0.164 --
obs-14443 99.841 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.451 Å2
Baniso -1Baniso -2Baniso -3
1-1.274 Å20.637 Å20 Å2
2--1.274 Å20 Å2
3----4.132 Å2
Refinement stepCycle: LAST / Resolution: 1.45→65.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms511 0 11 91 613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013555
X-RAY DIFFRACTIONr_bond_other_d0.0020.017541
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.656747
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5861253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.829570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.27819.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30115101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.083157
X-RAY DIFFRACTIONr_chiral_restr0.0720.265
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02625
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02132
X-RAY DIFFRACTIONr_nbd_refined0.1920.292
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.2495
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2249
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4610.29
X-RAY DIFFRACTIONr_nbd_other0.3070.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.28
X-RAY DIFFRACTIONr_mcbond_it3.5843.369259
X-RAY DIFFRACTIONr_mcbond_other3.3423.346258
X-RAY DIFFRACTIONr_mcangle_it4.055.043324
X-RAY DIFFRACTIONr_mcangle_other4.0485.056325
X-RAY DIFFRACTIONr_scbond_it5.4263.994295
X-RAY DIFFRACTIONr_scbond_other5.4193.998296
X-RAY DIFFRACTIONr_scangle_it6.6035.767418
X-RAY DIFFRACTIONr_scangle_other6.5955.77419
X-RAY DIFFRACTIONr_lrange_it6.78242.086616
X-RAY DIFFRACTIONr_lrange_other6.77842.136617
X-RAY DIFFRACTIONr_rigid_bond_restr4.44931094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.45-1.4880.645490.4889940.49510520.7740.81799.14450.477
1.488-1.5280.36390.4169790.41310210.9280.89499.70620.396
1.528-1.5730.406520.3079350.3129880.9240.94399.89880.279
1.573-1.6210.265550.269190.269750.9240.95699.89740.23
1.621-1.6740.234620.2128860.2139490.9520.96799.89460.179
1.674-1.7330.246350.198500.1928870.9390.96199.77450.156
1.733-1.7980.222340.1768510.1788850.9550.9611000.148
1.798-1.8720.19360.1498170.1518540.9630.96699.88290.127
1.872-1.9550.253410.1337660.1388070.9460.9731000.123
1.955-2.050.199380.1467670.1498050.9580.971000.139
2.05-2.1610.227380.1697030.1737410.9580.9641000.169
2.161-2.2920.197460.1556560.1587020.9570.9671000.161
2.292-2.450.182280.1376430.1396730.960.97399.70280.146
2.45-2.6460.228330.1265890.1316230.9630.97699.83950.141
2.646-2.8980.194290.1365370.1395660.9560.9721000.159
2.898-3.2390.168270.1545060.1555330.970.9631000.182
3.239-3.7390.284200.1664510.1714730.9160.9699.57720.2
3.739-4.5750.215210.1383890.1414100.9630.9761000.184
4.575-6.4550.196170.1613060.1633230.9660.9751000.237
6.455-65.740.322160.21830.2081990.9260.9611000.254

+
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