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- PDB-3t5x: PCID2:DSS1 Structure -

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Basic information

Entry
Database: PDB / ID: 3t5x
TitlePCID2:DSS1 Structure
Components
  • 26S proteasome complex subunit DSS1
  • PCI domain-containing protein 2
KeywordsTRANSCRIPTION / PCI / mRNA nuclear export
Function / homology
Function and homology information


negative regulation of lymphoid progenitor cell differentiation / negative regulation of transcription initiation by RNA polymerase II / positive regulation of mitotic cell cycle spindle assembly checkpoint / heterochromatin organization / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear pore nuclear basket / integrator complex ...negative regulation of lymphoid progenitor cell differentiation / negative regulation of transcription initiation by RNA polymerase II / positive regulation of mitotic cell cycle spindle assembly checkpoint / heterochromatin organization / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear pore nuclear basket / integrator complex / proteasome regulatory particle, lid subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Cross-presentation of soluble exogenous antigens (endosomes) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / positive regulation of B cell differentiation / Somitogenesis / poly(A)+ mRNA export from nucleus / Impaired BRCA2 binding to RAD51 / negative regulation of gene expression, epigenetic / Presynaptic phase of homologous DNA pairing and strand exchange / proteasome assembly / mRNA export from nucleus / spleen development / 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 / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / transcription elongation by RNA polymerase II / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / double-strand break repair via homologous recombination / 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 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / HDR through Homologous Recombination (HRR) / 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 / Regulation of RUNX2 expression and activity / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / protein transport / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Csn12 family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Csn12 family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
26S proteasome complex subunit SEM1 / PCI domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.123 Å
AuthorsStewart, M. / Ellisdon, A.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural basis for the assembly and nucleic acid binding of the TREX-2 transcription-export complex.
Authors: Ellisdon, A.M. / Dimitrova, L. / Hurt, E. / Stewart, M.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PCI domain-containing protein 2
B: 26S proteasome complex subunit DSS1


Theoretical massNumber of molelcules
Total (without water)32,0102
Polymers32,0102
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-20 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.522, 70.522, 95.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PCI domain-containing protein 2 / CSN12-like protein


Mass: 23725.059 Da / Num. of mol.: 1 / Fragment: UNP residues 201-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCID2, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JVF3
#2: Protein 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot ...Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


Mass: 8284.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHFM1, DSS1, SHFDG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P60896
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25.5 % (w/v) PEG 2K MME, 0.95 M sodium formate, and 0.1 M MES (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 2010
RadiationMonochromator: na / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.12→30 Å / Num. all: 14568 / Num. obs: 14568 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Net I/σ(I): 14.1
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2146 / % possible all: 94.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXAutosolmodel building
PHENIX(phenix.refine: dev_764)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXAutosolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.123→29.084 Å / SU ML: 0.49 / σ(F): 1.35 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 728 5.01 %RANDOM
Rwork0.2048 ---
all0.2061 14568 --
obs0.2048 14526 90.87 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.866 Å2 / ksol: 0.453 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4576 Å2-0 Å2-0 Å2
2--3.4576 Å2-0 Å2
3----6.9151 Å2
Refinement stepCycle: LAST / Resolution: 2.123→29.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 0 33 1894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031903
X-RAY DIFFRACTIONf_angle_d0.6512563
X-RAY DIFFRACTIONf_dihedral_angle_d13.115708
X-RAY DIFFRACTIONf_chiral_restr0.039284
X-RAY DIFFRACTIONf_plane_restr0.002319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1232-2.28710.28251170.24962400X-RAY DIFFRACTION81
2.2871-2.51710.25321680.21543005X-RAY DIFFRACTION100
2.5171-2.88110.2731400.20392681X-RAY DIFFRACTION90
2.8811-3.62880.23121640.20432902X-RAY DIFFRACTION96
3.6288-29.08650.20621390.19682810X-RAY DIFFRACTION88

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