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- PDB-7nzd: Fourth SH3 domain of POSH (Plenty of SH3 Domains protein) -

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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 / response to aldosterone / RHOV GTPase cycle / protein autoubiquitination / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / neuron migration ...regulation of CD4-positive, alpha-beta T cell differentiation / regulation of CD8-positive, alpha-beta T cell proliferation / MAP-kinase scaffold activity / response to aldosterone / RHOV GTPase cycle / protein autoubiquitination / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / neuron migration / 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 / zinc 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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