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- PDB-3h4m: AAA ATPase domain of the proteasome- activating nucleotidase -

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Basic information

Entry
Database: PDB / ID: 3h4m
TitleAAA ATPase domain of the proteasome- activating nucleotidase
ComponentsProteasome-activating nucleotidase
KeywordsHYDROLASE / ATPase / proteasome / PAN / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / CTPase activity / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasomal protein catabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / GTPase activity ...proteasome-activating nucleotidase complex / CTPase activity / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasomal protein catabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / GTPase activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
Proteasome-activating nucleotidase PAN / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) ...Proteasome-activating nucleotidase PAN / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Proteasome-activating nucleotidase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.106 Å
AuthorsJeffrey, P. / Zhang, F. / Hu, M. / Tian, G. / Zhang, P. / Finley, D. / Shi, Y.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural Insights into the Regulatory Particle of the Proteasome from Methanocaldococcus jannaschii.
Authors: Zhang, F. / Hu, M. / Tian, G. / Zhang, P. / Finley, D. / Jeffrey, P.D. / Shi, Y.
History
DepositionApr 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome-activating nucleotidase
B: Proteasome-activating nucleotidase
C: Proteasome-activating nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3886
Polymers96,1063
Non-polymers1,2823
Water00
1
A: Proteasome-activating nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4632
Polymers32,0351
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proteasome-activating nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4632
Polymers32,0351
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Proteasome-activating nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4632
Polymers32,0351
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.425, 116.425, 164.169
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A158 - 302
2115B158 - 302
3115C158 - 302
1215A309 - 340
2215B309 - 340
3215C309 - 340
1125A341 - 418
2125B341 - 418
3125C341 - 418
1135A419
2135B419
3135C419

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Proteasome-activating nucleotidase / Proteasome regulatory subunit


Mass: 32035.301 Da / Num. of mol.: 3 / Fragment: PAN ATPase domain (155-430)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: pan, MJ1176 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q58576
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M NaOAc, pH 4.6, and 0.65 M NH4H2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 22762 / Num. obs: 22762 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.084 / Net I/σ(I): 19.7
Reflection shellResolution: 3.1→3.21 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.523 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.4.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.106→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 56.334 / SU ML: 0.469 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27746 1092 5 %RANDOM
Rwork0.22064 ---
all0.22346 20697 --
obs0.22346 20697 95.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 101.078 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0.49 Å20 Å2
2---0.99 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 3.106→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6081 0 81 0 6162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226243
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4272.0218412
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50224.598261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.693151221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1291551
X-RAY DIFFRACTIONr_chiral_restr0.0950.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214524
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5441.53891
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04726282
X-RAY DIFFRACTIONr_scbond_it1.51532352
X-RAY DIFFRACTIONr_scangle_it2.6574.52130
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
11A708medium positional0.390.5
11B708medium positional0.370.5
11C708medium positional0.360.5
22A312medium positional0.240.5
22B312medium positional0.260.5
22C312medium positional0.320.5
11A661loose positional0.685
11B661loose positional0.675
11C661loose positional0.735
22A303loose positional0.565
22B303loose positional0.625
22C303loose positional0.665
33A27loose positional0.235
33B27loose positional0.195
33C27loose positional0.365
11A708medium thermal0.622
11B708medium thermal0.552
11C708medium thermal0.542
22A312medium thermal0.422
22B312medium thermal0.472
22C312medium thermal0.332
11A661loose thermal0.8610
11B661loose thermal0.8710
11C661loose thermal0.7710
22A303loose thermal0.7510
22B303loose thermal0.9310
22C303loose thermal0.7810
33A27loose thermal3.3710
33B27loose thermal13.8910
33C27loose thermal13.0410
LS refinement shellResolution: 3.106→3.187 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 77 -
Rwork0.284 1349 -
obs--86.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6279-3.78981.3588.64820.43951.9484-0.1362-0.0602-0.01090.39160.0852-0.6422-0.16410.07080.0509-0.0830.2544-0.3508-0.46680.0277-0.293713.29-49.751-9.675
29.598-4.96083.60689.4226-2.74445.2202-0.7023-1.1253-0.25760.56410.55551.13150.0286-0.55510.14670.02750.3687-0.2577-0.4103-0.1342-0.2433-13.408-32.14-11.072
38.50392.00231.67926.09780.82124.09860.32430.5185-1.4263-0.1461-0.0621-0.54430.58150.2774-0.2621-0.3459-0.0494-0.2203-0.5687-0.0132-0.317743.266-86.605-4.302
47.06964.27414.39656.14494.24747.5756-0.66311.06-0.0195-0.70220.4918-0.5172-0.66191.06360.1713-0.3497-0.2866-0.1019-0.41120.3217-0.367362.644-61.4650.995
56.8961-1.49461.49747.479-3.29855.3309-0.471-1.1054-0.50970.15250.67591.3244-0.2175-1.2327-0.205-0.0830.3310.00570.38510.2329-0.103221.621-66.58620.54
61.6614-0.13850.81318.1237-2.15558.2314-0.9365-0.50491.10271.16570.0848-0.339-1.6598-0.05130.85180.86740.3522-0.7744-0.0809-0.22330.405627.242-35.71913.214
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A158 - 340
2X-RAY DIFFRACTION2A341 - 418
3X-RAY DIFFRACTION3B158 - 340
4X-RAY DIFFRACTION4B341 - 418
5X-RAY DIFFRACTION5C158 - 340
6X-RAY DIFFRACTION6C341 - 418

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