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- PDB-6jpt: Crystal structure of human PAC3 homodimer (trigonal form) -

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Basic information

Entry
Database: PDB / ID: 6jpt
TitleCrystal structure of human PAC3 homodimer (trigonal form)
ComponentsProteasome assembly chaperone 3
KeywordsCHAPERONE / PROTEASOME ASSEMBLY CHAPERONE
Function / homology
Function and homology information


chaperone-mediated protein complex assembly / proteasome assembly / molecular adaptor activity / protein-containing complex binding / protein-containing complex
Similarity search - Function
Ribosomal Protein S5; domain 2 - #90 / Proteasome assembly chaperone 3 / Proteasome assembly chaperone 3 / : / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / THIOCYANATE ION / Proteasome assembly chaperone 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsSatoh, T. / Yagi-Utsumi, M. / Okamoto, K. / Kurimoto, E. / Tanaka, K. / Kato, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP26460051, JP25102008, JP15H02491 Japan
CitationJournal: Int J Mol Sci / Year: 2019
Title: Molecular and Structural Basis of the Proteasome alpha Subunit Assembly Mechanism Mediated by the Proteasome-Assembling Chaperone PAC3-PAC4 Heterodimer.
Authors: Satoh, T. / Yagi-Utsumi, M. / Okamoto, K. / Kurimoto, E. / Tanaka, K. / Kato, K.
History
DepositionMar 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasome assembly chaperone 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2163
Polymers13,1181
Non-polymers972
Water2,990166
1
A: Proteasome assembly chaperone 3
hetero molecules

A: Proteasome assembly chaperone 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4316
Polymers26,2372
Non-polymers1944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3230 Å2
ΔGint-24 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.229, 71.229, 47.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

21A-443-

HOH

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Components

#1: Protein Proteasome assembly chaperone 3 / hPAC3


Mass: 13118.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMG3, C7orf48, PAC3 / Plasmid: PRSF-DUET I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BT73
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG2000 monomethyl ether, 0.1 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.96→47.07 Å / Num. obs: 83927 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Net I/σ(I): 17.1
Reflection shellResolution: 0.96→0.98 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.162 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4048 / CC1/2: 0.606 / Rpim(I) all: 0.579 / Rrim(I) all: 1.303 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z5E

2z5e


Resolution: 0.96→14.655 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.19
RfactorNum. reflection% reflection
Rfree0.1458 1999 2.38 %
Rwork0.1359 --
obs0.1362 83857 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.96→14.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 4 166 1079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008939
X-RAY DIFFRACTIONf_angle_d1.0511282
X-RAY DIFFRACTIONf_dihedral_angle_d18.971348
X-RAY DIFFRACTIONf_chiral_restr0.088167
X-RAY DIFFRACTIONf_plane_restr0.008159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9602-0.98420.26451380.27295706X-RAY DIFFRACTION98
0.9842-1.01080.24591390.21845781X-RAY DIFFRACTION100
1.0108-1.04050.23571460.19945847X-RAY DIFFRACTION100
1.0405-1.07410.17781430.15675793X-RAY DIFFRACTION100
1.0741-1.11250.12911420.12975806X-RAY DIFFRACTION100
1.1125-1.1570.12881420.11515831X-RAY DIFFRACTION100
1.157-1.20960.11711420.115826X-RAY DIFFRACTION100
1.2096-1.27340.12051430.1125855X-RAY DIFFRACTION100
1.2734-1.35310.12461440.11035808X-RAY DIFFRACTION100
1.3531-1.45750.12871420.11315848X-RAY DIFFRACTION100
1.4575-1.6040.11981430.11315851X-RAY DIFFRACTION100
1.604-1.83570.13321450.12175902X-RAY DIFFRACTION100
1.8357-2.31140.14391440.13245929X-RAY DIFFRACTION100
2.3114-14.65690.15661460.15076075X-RAY DIFFRACTION100

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