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- PDB-3aji: Structure of Gankyrin-S6ATPase photo-cross-linked site-specifical... -

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Basic information

Entry
Database: PDB / ID: 3aji
TitleStructure of Gankyrin-S6ATPase photo-cross-linked site-specifically, and incoporated by genetic code expansion
Components
  • 26S proteasome non-ATPase regulatory subunit 10
  • Proteasome (Prosome, macropain) 26S subunit, ATPase, 4
KeywordsCHAPERONE/PROTEIN BINDING / Gankyrin / S6 atpase / p-benzoyl-L-phenylalanine / pbpa / amber suppression / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / CHAPERONE-PROTEIN BINDING complex
Function / homology
Function and homology information


: / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 ...: / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Degradation of AXIN / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / UCH proteinases / Orc1 removal from chromatin / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / Hedgehog ligand biogenesis / TNFR2 non-canonical NF-kB pathway / cytoplasmic sequestering of NF-kappaB / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / Degradation of beta-catenin by the destruction complex / Activation of NF-kappaB in B cells / The role of GTSE1 in G2/M progression after G2 checkpoint / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Separation of Sister Chromatids / proteasome regulatory particle assembly / Downstream TCR signaling / KEAP1-NFE2L2 pathway / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / ABC-family proteins mediated transport / proteasome accessory complex / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / intermediate filament cytoskeleton / negative regulation of MAPK cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of release of cytochrome c from mitochondria / negative regulation of DNA damage response, signal transduction by p53 class mediator / blastocyst development / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / inclusion body / cytoskeletal protein binding / proteasome complex / positive regulation of protein ubiquitination / protein localization to plasma membrane / protein catabolic process / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of cell growth / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / cytoskeleton / neuron projection / synapse / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit P45-like / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Ankyrin repeat-containing domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. ...26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit P45-like / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Ankyrin repeat-containing domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Ankyrin repeat / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / ATPase, AAA-type, core / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
26S proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSato, S. / Mimasu, S. / Sato, A. / Hino, N. / Sakamoto, K. / Umehara, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochemistry / Year: 2011
Title: Crystallographic study of a site-specifically cross-linked protein complex with a genetically incorporated photoreactive amino acid
Authors: Sato, S. / Mimasu, S. / Sato, A. / Hino, N. / Sakamoto, K. / Umehara, T. / Yokoyama, S.
History
DepositionJun 7, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
B: Proteasome (Prosome, macropain) 26S subunit, ATPase, 4
C: 26S proteasome non-ATPase regulatory subunit 10
D: Proteasome (Prosome, macropain) 26S subunit, ATPase, 4


Theoretical massNumber of molelcules
Total (without water)69,9504
Polymers69,9504
Non-polymers00
Water5,891327
1
A: 26S proteasome non-ATPase regulatory subunit 10
B: Proteasome (Prosome, macropain) 26S subunit, ATPase, 4


Theoretical massNumber of molelcules
Total (without water)34,9752
Polymers34,9752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint1 kcal/mol
Surface area13260 Å2
MethodPISA
2
C: 26S proteasome non-ATPase regulatory subunit 10
D: Proteasome (Prosome, macropain) 26S subunit, ATPase, 4


Theoretical massNumber of molelcules
Total (without water)34,9752
Polymers34,9752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint0 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.164, 103.164, 154.993
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-253-

HOH

21C-263-

HOH

31C-266-

HOH

41D-238-

HOH

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Components

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


Mass: 25181.635 Da / Num. of mol.: 2 / Mutation: R85F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psmd10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2X2
#2: Protein Proteasome (Prosome, macropain) 26S subunit, ATPase, 4 / S6C


Mass: 9793.156 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psmc4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZWN9, UniProt: P54775*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 85TH NON-NATURAL RESIDUE IS THE PHOTO REACTED VERSION OF PBPA INCOPORATED BY THE GENETIC CODE ...THE 85TH NON-NATURAL RESIDUE IS THE PHOTO REACTED VERSION OF PBPA INCOPORATED BY THE GENETIC CODE EXPANSION, AND THE 356TH RESIDUE IS THE PHOTO-COVALENT-BONDED PBPA ON GLUTAMIC ACID.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 31% polyethylene glycol 4000, 0.26M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONSPring-8 BL41XU1
SYNCHROTRONSPring-8 BL26B22
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDDec 15, 2008
RAYONIX MX-2252CCDOct 24, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 38604 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.098 / Net I/σ(I): 20.7
Reflection shellResolution: 2.05→2.18 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 6083 / Rsym value: 0.454 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DVW

2dvw


Resolution: 2.05→42.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2665091.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1914 5 %RANDOM
Rwork0.171 ---
obs0.171 38604 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.4515 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.13 Å20 Å20 Å2
2--4.13 Å20 Å2
3----8.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.05→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 0 327 4995
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.032
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 347 5.4 %
Rwork0.208 6083 -
obs-6083 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2pbpa.parampbpa.top
X-RAY DIFFRACTION3water_rep.param

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