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- PDB-2wg5: Proteasome-Activating Nucleotidase (PAN) N-domain (57-134) from A... -

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Basic information

Entry
Database: PDB / ID: 2wg5
TitleProteasome-Activating Nucleotidase (PAN) N-domain (57-134) from Archaeoglobus fulgidus fused to GCN4
ComponentsGENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
KeywordsTRANSCRIPTION / HYDROLASE / TRANSCRIPTION HYDROLASE COMPLEX / NUCLEOTIDE-BINDING / SUBSTRATE RECOGNITION / COILED COIL / AAA PROTEIN / CHAPERONE ACTIVITY / ATPASE / OB FOLD / CYTOPLASM / PROTEASOME / ATP-BINDING AMINO-ACID BIOSYNTHESIS / TRANSCRIPTION REGULATION / NUCLEUS / DNA-BINDING / ACTIVATOR / PHOSPHOPROTEIN
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...proteasome-activating nucleotidase complex / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process / protein unfolding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / proteasomal protein catabolic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Proteasome-activating nucleotidase PAN / : / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / : / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain ...Proteasome-activating nucleotidase PAN / : / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / : / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleic acid-binding proteins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Proteasome-activating nucleotidase / General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
ARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHartmann, M.D. / Djuranovic, S. / Ursinus, A. / Zeth, K. / Lupas, A.N.
CitationJournal: Mol.Cell / Year: 2009
Title: Structure and Activity of the N-Terminal Substrate Recognition Domains in Proteasomal Atpases.
Authors: Djuranovic, S. / Hartmann, M.D. / Habeck, M. / Ursinus, A. / Zwickl, P. / Martin, J. / Lupas, A.N. / Zeth, K.
History
DepositionApr 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
B: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
C: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
D: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
E: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
F: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
G: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
H: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
I: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
J: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
K: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
L: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE


Theoretical massNumber of molelcules
Total (without water)148,92112
Polymers148,92112
Non-polymers00
Water7,710428
1
A: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
B: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
C: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
D: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
E: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
F: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE


Theoretical massNumber of molelcules
Total (without water)74,4616
Polymers74,4616
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12040 Å2
ΔGint-81.21 kcal/mol
Surface area27670 Å2
MethodPISA
2
G: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
H: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
I: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
J: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
K: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE
L: GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE


Theoretical massNumber of molelcules
Total (without water)74,4616
Polymers74,4616
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-80.24 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.390, 91.950, 103.220
Angle α, β, γ (deg.)90.00, 119.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12G
22I
32K
13B
23D
33F
14H
24J
34L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 300
2111C1 - 300
3111E1 - 300
1121G1 - 300
2121I1 - 300
3121K1 - 300
1131B1 - 300
2131D1 - 300
3131F1 - 300
1141H1 - 300
2141J1 - 300
3141L1 - 300

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE


Mass: 12410.123 Da / Num. of mol.: 12
Fragment: N-DOMAIN (57-134) FUSED TO GCN4, RESIDUES 33-56,57-134
Source method: isolated from a genetically manipulated source
Details: NATIVE COILED COIL SUBSTITUTED BY GCN4
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069, UniProt: O28303, EC: 3.6.4.8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFUSION PROTEIN

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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: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growDetails: 100 MM TRIS PH 9.0, 1 M NH4H2PO4, 25% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.071
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 2.1→34.36 Å / Num. obs: 97626 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.28 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.95
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 4.23 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.26 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WFW

2wfw


Resolution: 2.1→34.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22742 4853 5 %RANDOM
Rwork0.19753 ---
obs0.19901 92772 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0.17 Å2
2--0.74 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8029 0 0 428 8457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228125
X-RAY DIFFRACTIONr_bond_other_d00.025422
X-RAY DIFFRACTIONr_angle_refined_deg1.628211042
X-RAY DIFFRACTIONr_angle_other_deg4.229313447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56351032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.04725.727337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.745151487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0651548
X-RAY DIFFRACTIONr_chiral_restr0.10.21368
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028836
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021344
X-RAY DIFFRACTIONr_nbd_refined0.2050.21577
X-RAY DIFFRACTIONr_nbd_other0.2330.25032
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23928
X-RAY DIFFRACTIONr_nbtor_other0.1120.24061
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2396
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0280.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.30865220
X-RAY DIFFRACTIONr_mcbond_other062064
X-RAY DIFFRACTIONr_mcangle_it6.37598512
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.322122905
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it11.533182530
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1119tight positional0.020.05
12C1119tight positional0.020.05
13E1119tight positional0.020.05
21G1134tight positional0.020.05
22I1134tight positional0.020.05
23K1134tight positional0.020.05
31B1129tight positional0.020.05
32D1129tight positional0.020.05
33F1129tight positional0.020.05
41H1096tight positional0.020.05
42J1096tight positional0.020.05
43L1096tight positional0.020.05
11A1119tight thermal0.150.5
12C1119tight thermal0.150.5
13E1119tight thermal0.140.5
21G1134tight thermal0.130.5
22I1134tight thermal0.140.5
23K1134tight thermal0.140.5
31B1129tight thermal0.150.5
32D1129tight thermal0.160.5
33F1129tight thermal0.150.5
41H1096tight thermal0.130.5
42J1096tight thermal0.140.5
43L1096tight thermal0.140.5
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 371 -
Rwork0.273 6825 -
obs--99.46 %

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