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- PDB-7ynx: Crystal structure of Pirh2 bound to poly-Ala peptide -

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Basic information

Entry
Database: PDB / ID: 7ynx
TitleCrystal structure of Pirh2 bound to poly-Ala peptide
ComponentsRING finger and CHY zinc finger domain-containing protein 1
KeywordsCYTOSOLIC PROTEIN / E3 LIGASE / LIGASE
Function / homology
Function and homology information


error-free translesion synthesis / protein autoubiquitination / ubiquitin ligase complex / rescue of stalled ribosome / positive regulation of protein ubiquitination / Translesion Synthesis by POLH / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation ...error-free translesion synthesis / protein autoubiquitination / ubiquitin ligase complex / rescue of stalled ribosome / positive regulation of protein ubiquitination / Translesion Synthesis by POLH / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear speck / intracellular membrane-bounded organelle / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Zinc finger, CHY-type / Zinc finger, CTCHY-type / Zinc finger, CHY-type superfamily / Zinc finger, CTCHY-type superfamily / RCHY1, zinc-ribbon / CHY zinc finger / Zinc-ribbon / Zinc finger CHY-type profile. / Zinc finger CTCHY-type profile. / Ring finger domain ...Zinc finger, CHY-type / Zinc finger, CTCHY-type / Zinc finger, CHY-type superfamily / Zinc finger, CTCHY-type superfamily / RCHY1, zinc-ribbon / CHY zinc finger / Zinc-ribbon / Zinc finger CHY-type profile. / Zinc finger CTCHY-type profile. / Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RING finger and CHY zinc finger domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsDong, C. / Yan, X. / Li, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900865 China
National Natural Science Foundation of China (NSFC)32071193 China
National Natural Science Foundation of China (NSFC)81874039 China
CitationJournal: Nat Commun / Year: 2023
Title: Recognition of an Ala-rich C-degron by the E3 ligase Pirh2.
Authors: Wang, X. / Li, Y. / Yan, X. / Yang, Q. / Zhang, B. / Zhang, Y. / Yuan, X. / Jiang, C. / Chen, D. / Liu, Q. / Liu, T. / Mi, W. / Yu, Y. / Dong, C.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.details
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RING finger and CHY zinc finger domain-containing protein 1
B: RING finger and CHY zinc finger domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,63935
Polymers45,8372
Non-polymers1,80333
Water2,792155
1
A: RING finger and CHY zinc finger domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,79518
Polymers22,9181
Non-polymers87617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RING finger and CHY zinc finger domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,84517
Polymers22,9181
Non-polymers92616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.470, 80.270, 84.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RING finger and CHY zinc finger domain-containing protein 1 / Androgen receptor N-terminal-interacting protein / CH-rich-interacting match with PLAG1 / E3 ...Androgen receptor N-terminal-interacting protein / CH-rich-interacting match with PLAG1 / E3 ubiquitin-protein ligase Pirh2 / RING finger protein 199 / RING-type E3 ubiquitin transferase RCHY1 / Zinc finger protein 363 / p53-induced RING-H2 protein / hPirh2


Mass: 22918.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the last 6 residues mimic poly-ala degron / Source: (gene. exp.) Homo sapiens (human) / Gene: RCHY1, ARNIP, CHIMP, PIRH2, RNF199, ZNF363 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96PM5, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH7.5, 0.1 M NaCl, 1.6 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.28277 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28277 Å / Relative weight: 1
ReflectionResolution: 2.3→37.52 Å / Num. obs: 21662 / % possible obs: 81.14 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.2467 / Net I/σ(I): 8.62
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 1.328 / Num. unique obs: 2119

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→37.52 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 1787 9.1 %
Rwork0.2157 17847 -
obs0.2201 19634 90.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.71 Å2 / Biso mean: 32.4996 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: final / Resolution: 2.3→37.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 53 155 3174
Biso mean--55.06 35.1 -
Num. residues----376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.360.33391090.2591198130781
2.36-2.430.3481270.25681233136082
2.43-2.510.30261140.26111279139386
2.51-2.60.33291310.23961255138685
2.6-2.70.28371340.24491277141186
2.7-2.830.30951370.24141333147090
2.83-2.980.28231330.22971365149890
2.98-3.160.2821450.22081419156494
3.16-3.410.29841460.21161420156695
3.41-3.750.25781470.19851463161097
3.75-4.290.21291420.17931499164197
4.29-5.40.21551540.19381522167698
5.4-37.520.2361680.22261584175297

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