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- PDB-7vxw: Snapshots of Human PSMD10(Gankyrin) unfolding by urea: 1 hour inc... -

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Basic information

Entry
Database: PDB / ID: 7vxw
TitleSnapshots of Human PSMD10(Gankyrin) unfolding by urea: 1 hour incubation
Components26S proteasome non-ATPase regulatory subunit 10
KeywordsONCOPROTEIN / Proteasomal Chaperone / Urea denaturation
Function / homology
Function and homology information


cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / protein localization to chromosome, telomeric region / negative regulation of MAPK cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of release of cytochrome c from mitochondria ...cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / protein localization to chromosome, telomeric region / negative regulation of MAPK cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of release of cytochrome c from mitochondria / positive regulation of telomere capping / negative regulation of DNA damage response, signal transduction by p53 class mediator / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / NAD+-protein poly-ADP-ribosyltransferase activity / cytoskeletal protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / protein localization to plasma membrane / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / positive regulation of cell growth / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / cytoskeleton / Ub-specific processing proteases / neuron projection / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
UREA / 26S proteasome non-ATPase regulatory subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsMukund Sudharsan, M.G. / Dalvi, S. / Venkatraman, P.
Funding support India, 1items
OrganizationGrant numberCountry
Other government5/13/62/2020-NCD-III India
CitationJournal: Protein Sci. / Year: 2022
Title: Snapshots of urea-induced early structural changes and unfolding of an ankyrin repeat protein at atomic resolution.
Authors: Medur Gurushankar, M.S. / Dalvi, S. / Venkatraman, P.
History
DepositionNov 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 26S proteasome non-ATPase regulatory subunit 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6404
Polymers24,4601
Non-polymers1803
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-0 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.190, 60.190, 122.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 26S proteasome non-ATPase regulatory subunit 10 / 26S proteasome regulatory subunit p28 / Gankyrin / p28(GANK)


Mass: 24459.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gankyrin pBluescript II SK (1) construct (kind gift from Dr. Jun Fujita, Kyoto University)
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD10 / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2DE3 / References: UniProt: O75832
#2: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% Tacsimate pH7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 9, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→52.13 Å / Num. obs: 12878 / % possible obs: 96.7 % / Redundancy: 8.7 % / Rpim(I) all: 0.097 / Rrim(I) all: 0.293 / Rsym value: 0.276 / Net I/av σ(I): 2.7 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.224-2.338.41.6080.516260.571.7091.60885.2
2.33-2.478.81.3050.617710.4551.3841.30598
2.47-2.658.81.1440.716520.3981.2121.14498.1
2.65-2.868.80.801115660.280.850.80198.6
2.86-3.138.80.5421.414400.1910.5750.54298.7
3.13-3.58.80.2882.713380.1010.3060.28899
3.5-4.048.70.1435.311750.050.1520.14399.5
4.04-4.958.60.0938.110180.0330.0980.09399.4
4.95-78.40.0967.58090.0350.1030.09699.8
7-52.1267.80.02923.84830.0110.0310.02999.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOH

1uoh


Resolution: 2.22→52.13 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.859 / WRfactor Rfree: 0.2811 / WRfactor Rwork: 0.1936 / FOM work R set: 0.6482 / SU B: 14.75 / SU ML: 0.326 / SU R Cruickshank DPI: 0.3294 / SU Rfree: 0.2886 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3266 1291 10 %RANDOM
Rwork0.2417 ---
obs0.2502 11587 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.76 Å2 / Biso mean: 41.543 Å2 / Biso min: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.22→52.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 12 34 1739
Biso mean--67.36 30.85 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131658
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161594
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6222243
X-RAY DIFFRACTIONr_angle_other_deg1.2891.5793640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83924.15465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50215270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.183155
X-RAY DIFFRACTIONr_chiral_restr0.0610.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
LS refinement shellResolution: 2.224→2.281 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 87 -
Rwork0.397 775 -
all-862 -
obs--91.51 %

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