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- PDB-7vy4: Snapshots of Human PSMD10(Gankyrin) unfolding by urea: 2 hours in... -

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Basic information

Entry
Database: PDB / ID: 7vy4
TitleSnapshots of Human PSMD10(Gankyrin) unfolding by urea: 2 hours incubation
Components26S proteasome non-ATPase regulatory subunit 10
KeywordsONCOPROTEIN / Proteasomal Chaperone / Urea denaturation
Function / homology
Function and homology information


proteasome regulatory particle assembly / positive regulation of cyclin-dependent protein serine/threonine kinase activity / Proteasome assembly / negative regulation of NF-kappaB transcription factor activity / transcription factor binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of MAPK cascade / proteasome complex / positive regulation of protein ubiquitination ...proteasome regulatory particle assembly / positive regulation of cyclin-dependent protein serine/threonine kinase activity / Proteasome assembly / negative regulation of NF-kappaB transcription factor activity / transcription factor binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of MAPK cascade / proteasome complex / positive regulation of protein ubiquitination / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / positive regulation of cell growth / RNA polymerase II-specific DNA-binding transcription factor binding / cytoskeleton / cilium / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleus / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,7606
Polymers24,4601
Non-polymers3005
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-1 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.300, 60.300, 122.310
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.: 5 / 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: 2.62 Å3/Da / Density meas: 47 Mg/m3 / Density % sol: 53.13 %
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 10, 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→52.221 Å / Num. obs: 13221 / % possible obs: 98.2 % / Redundancy: 8.6 % / Rpim(I) all: 0.099 / Rrim(I) all: 0.295 / Rsym value: 0.277 / Net I/av σ(I): 2.7 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.224-2.338.21.7020.516880.6141.8131.70288.1
2.33-2.478.71.3320.618290.4721.4141.332100
2.47-2.658.71.0970.717050.3881.1651.097100
2.65-2.868.70.785116040.2780.8340.785100
2.86-3.138.70.551.314720.1950.5840.55100
3.13-3.58.70.2782.813750.0990.2960.278100
3.5-4.048.70.1395.512020.0490.1480.139100
4.04-4.958.60.0928.110280.0330.0970.092100
4.95-78.40.1066.78160.0380.1130.106100
7-52.2217.70.03320.55020.0120.0350.03399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1uoh


Resolution: 2.22→52.22 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.874 / SU B: 12.73 / SU ML: 0.286 / SU R Cruickshank DPI: 0.3214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3121 1308 9.9 %RANDOM
Rwork0.2406 ---
obs0.2475 11877 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.04 Å2 / Biso mean: 38.776 Å2 / Biso min: 17.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 2.22→52.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 20 34 1747
Biso mean--54.92 31.57 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131682
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161588
X-RAY DIFFRACTIONr_angle_refined_deg1.671.6222275
X-RAY DIFFRACTIONr_angle_other_deg1.7241.5773643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1595222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11324.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90115277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.503155
X-RAY DIFFRACTIONr_chiral_restr0.0640.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021940
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
Rfree0.377 89 -
Rwork0.406 814 -
all-903 -
obs--95.86 %

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