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- PDB-7nzc: First SH3 domain of POSH (Plenty of SH3 Domains protein) -

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Basic information

Entry
Database: PDB / ID: 7nzc
TitleFirst 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 / protein autoubiquitination / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / neuron migration / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process ...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 / protein autoubiquitination / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / neuron migration / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / 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 / 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 ...E3 ubiquitin-protein ligase SH3RF1, second SH3 domain / SH3RF1/SH3RF3, fourth SH3 domain / 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
E3 ubiquitin-protein ligase SH3RF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.111 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,5382
Polymers7,2991
Non-polymers2381
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint1 kcal/mol
Surface area4390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.962, 35.962, 181.333
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11AAA-429-

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: 7299.355 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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.4 Å3/Da / Density % sol: 47.5 % / Description: hexagonal shape
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 0.2 M NaF, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 1, 2019 / Details: Monochromators
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.11→30.7 Å / Num. obs: 2677 / % possible obs: 96 % / Redundancy: 19.4 % / CC1/2: 0.999 / Net I/σ(I): 26.1
Reflection shellResolution: 1.11→1.13 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 404 / CC1/2: 0.565

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: modified 2SRC

2src


Resolution: 1.111→30.694 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.746 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.034
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1775 1321 4.956 %
Rwork0.1468 25335 -
all0.148 --
obs-26656 92.578 %
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: 17.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.043 Å20.022 Å20 Å2
2--0.043 Å20 Å2
3----0.141 Å2
Refinement stepCycle: LAST / Resolution: 1.111→30.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms502 0 15 138 655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013565
X-RAY DIFFRACTIONr_bond_other_d0.0010.017531
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.684771
X-RAY DIFFRACTIONr_angle_other_deg1.3881.6321245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.622570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.77223.12532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3261598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.468153
X-RAY DIFFRACTIONr_chiral_restr0.0810.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02119
X-RAY DIFFRACTIONr_nbd_refined0.2080.290
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.2496
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2258
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2260
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2113
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.27
X-RAY DIFFRACTIONr_nbd_other0.1550.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2530.212
X-RAY DIFFRACTIONr_mcbond_it16.4181.556256
X-RAY DIFFRACTIONr_mcbond_other16.451.557255
X-RAY DIFFRACTIONr_mcangle_it26.5342.046322
X-RAY DIFFRACTIONr_mcangle_other26.4932.045323
X-RAY DIFFRACTIONr_scbond_it18.7461.484309
X-RAY DIFFRACTIONr_scbond_other18.7451.484309
X-RAY DIFFRACTIONr_scangle_it24.8362.169445
X-RAY DIFFRACTIONr_scangle_other24.8092.174446
X-RAY DIFFRACTIONr_lrange_it26.46919.698690
X-RAY DIFFRACTIONr_lrange_other26.45119.721691
X-RAY DIFFRACTIONr_rigid_bond_restr3.12831096
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
1.111-1.1390.273270.2827150.28220550.8540.82336.10710.284
1.139-1.1710.242840.20314230.20520220.9330.9474.53020.189
1.171-1.2040.1461070.1516590.1519910.9650.96888.69910.134
1.204-1.2410.17970.13217260.13418970.9680.97296.09910.117
1.241-1.2820.156810.11617560.11818430.9740.97999.67440.104
1.282-1.3270.138810.10717170.10817980.9790.9831000.097
1.327-1.3770.118950.10116520.10217470.9830.9861000.092
1.377-1.4330.122890.10115750.10316650.9830.98599.93990.093
1.433-1.4970.124990.09715340.09916330.9840.9871000.091
1.497-1.5690.12680.09714720.09815400.9860.9871000.092
1.569-1.6540.128690.10614060.10714750.9830.9851000.102
1.654-1.7540.157680.11513370.11714050.9740.9821000.112
1.754-1.8750.162680.1212740.12213420.9790.9811000.121
1.875-2.0240.145450.13112100.13212550.9750.981000.135
2.024-2.2170.136520.1411050.1411570.9750.9771000.149
2.217-2.4770.155380.14910190.14910570.9710.9751000.162
2.477-2.8570.2450.1759170.1769620.9590.9651000.193
2.857-3.4910.216460.1787900.188360.9480.9641000.212
3.491-4.9060.2360.1556360.1576720.9640.9781000.201
4.906-30.6940.34260.2774110.2814390.9340.94699.54440.348

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