[English] 日本語
Yorodumi
- PDB-4ouh: Crystal structure of the FP domain of Human PI31 Proteasome Inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ouh
TitleCrystal structure of the FP domain of Human PI31 Proteasome Inhibitor
ComponentsProteasome inhibitor PI31 subunit
KeywordsPROTEIN BINDING / C-terminal extention alpha Helix / Proteasome Inhibitor
Function / homology
Function and homology information


negative regulation of proteasomal protein catabolic process / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / endopeptidase inhibitor activity / proteasome binding / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin ...negative regulation of proteasomal protein catabolic process / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / endopeptidase inhibitor activity / proteasome binding / 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 / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / 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 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 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 / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / protein heterodimerization activity / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / nucleoplasm / membrane / cytosol
Similarity search - Function
Protein Transport Mog1p; Chain A - #30 / PI31 proteasome regulator, C-terminal / Proteasome inhibitor PI31-like / PI31 proteasome regulator / PI31 proteasome regulator, N-terminal / PI31 proteasome regulator N-terminal / Protein Transport Mog1p; Chain A / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome inhibitor PI31 subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShang, J. / Huang, X. / Du, Z.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2015
Title: The FP domains of PI31 and Fbxo7 have the same protein fold but very different modes of protein-protein interaction.
Authors: Shang, J. / Huang, X. / Du, Z.
History
DepositionFeb 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Apr 1, 2015Group: Database references
Revision 1.4Apr 8, 2015Group: Database references
Revision 1.5Apr 22, 2015Group: Database references
Revision 1.6Apr 29, 2015Group: Database references
Revision 1.7May 20, 2015Group: Database references
Revision 1.8Feb 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome inhibitor PI31 subunit
B: Proteasome inhibitor PI31 subunit
C: Proteasome inhibitor PI31 subunit
D: Proteasome inhibitor PI31 subunit


Theoretical massNumber of molelcules
Total (without water)72,8384
Polymers72,8384
Non-polymers00
Water8,899494
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Proteasome inhibitor PI31 subunit
B: Proteasome inhibitor PI31 subunit


Theoretical massNumber of molelcules
Total (without water)36,4192
Polymers36,4192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-9 kcal/mol
Surface area14400 Å2
MethodPISA
3
C: Proteasome inhibitor PI31 subunit
D: Proteasome inhibitor PI31 subunit


Theoretical massNumber of molelcules
Total (without water)36,4192
Polymers36,4192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-8 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.830, 97.670, 108.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Proteasome inhibitor PI31 subunit / hPI31


Mass: 18209.475 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN PI31, PSMF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92530
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000, NaAc, KBr, pH 5.0, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→31.176 Å / Num. obs: 42700

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→31.176 Å / FOM work R set: 0.8455 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 2000 4.68 %
Rwork0.1864 --
obs0.1887 42700 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.55 Å2 / Biso mean: 28.92 Å2 / Biso min: 5.22 Å2
Refinement stepCycle: LAST / Resolution: 2→31.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 0 494 5142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044744
X-RAY DIFFRACTIONf_angle_d0.8776438
X-RAY DIFFRACTIONf_chiral_restr0.063723
X-RAY DIFFRACTIONf_plane_restr0.004827
X-RAY DIFFRACTIONf_dihedral_angle_d12.9891728
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.28251390.20862837297699
2.05-2.10540.26751410.20852865300699
2.1054-2.16740.23251390.195628452984100
2.1674-2.23730.2831410.18412870301199
2.2373-2.31720.23341420.19012865300799
2.3172-2.410.2631410.18628733014100
2.41-2.51960.23421420.195928913033100
2.5196-2.65240.2531410.187328913032100
2.6524-2.81850.23541430.198528953038100
2.8185-3.03590.28251430.193529043047100
3.0359-3.34110.25281430.192329353078100
3.3411-3.82390.23751460.168529513097100
3.8239-4.81480.19061450.158229723117100
4.8148-31.18020.21451540.19973106326099
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)
10.0276-0.00850.0230.0034-0.00560.01790.0004-0.05980.0195-0.06810.02520.01540.022-0.01540.0010.07770.00230.00620.0602-0.01010.063511.81458.9478106.7208
20.01010.00010.00080.0057-0.00030.0052-0.012-0.04630.03990.0270.0379-0.0259-0.0286-0.02350.00870.1060.01140.00950.0858-0.03240.111816.33718.8823112.3778
30.04-0.01150.03160.0068-0.00740.02140.0046-0.0421-0.04370.0466-0.0078-0.02070.0669-0.03050.00750.09210.0068-0.01040.0622-0.106-0.013322.02787.4637111.9241
40.0156-0.00520.00160.00250.00090.0034-0.04210.0232-0.0722-0.0524-0.01660.0187-0.0229-0.0139-0.00410.13390.011-0.01520.0766-0.00680.110614.56661.79298.4153
50.00150.00060.00210.00020.00020.0020.00580.01830.01650.04610.00110.00060.0085-0.003700.28550.0003-0.08660.25330.05770.250619.1125-1.9529123.7039
60.00820.0043-0.00080.00280.00240.0071-0.0176-0.0309-0.0252-0.0047-0.02330.01630.0299-0.0027-0.00410.10160.01860.00040.105-0.01510.0961-3.319913.2445109.8963
70.03960.06120.01360.09790.02390.0058-0.07790.02820.0202-0.0231-0.03030.0298-0.00030.049-0.04040.115-0.0091-0.00110.062-0.00840.0428-9.79838.4196102.3261
80.00140.00210.00170.00450.00020.00710.00320.0221-0.0413-0.00610.0207-0.03040.01470.00550.00530.08860.0256-0.02730.0751-0.09520.0907-9.78980.5804100.1921
90.0135-0.01490.00650.0198-0.01110.019-0.0067-0.03270.02220.011-0.00320.0142-0.0093-0.02460.01120.03250.02820.05840.0654-0.13180.1222-19.90564.9716106.8123
100.00150.0008-0.00240.0006-0.00190.0046-0.0163-0.0209-0.0109-0.0040.01080.00730.0078-0.0105-0.00020.1227-0.01820.03540.1198-0.04240.0657-18.9078.8021117.1315
110.0617-0.01990.02350.0137-0.00540.0095-0.0839-0.0670.00880.0287-0.0062-0.01010.0012-0.0018-0.02360.14170.01080.00470.1155-0.01440.0705-9.262912.7609118.9538
120.00130.0001-0.00290.00010.00030.0060.00080.0213-0.0081-0.0077-0.008-0.00520.0276-0.00310.00030.2257-0.03870.04790.1236-0.02130.2872-12.7312-10.6932108.943
130.05620.0248-0.00330.01080.00040.00080.0147-0.036-0.0521-0.00950.02220.02320.0252-0.0370.01590.0598-0.05480.0040.15320.25440.211-2.914428.489379.6155
140.00270.00220.00380.00110.00070.00430.0131-0.0197-0.0188-0.00790.010.00430.01570.02160.0420.11610.0063-0.01390.30070.21190.24161.625921.172788.329
150.0014-0.00270.00150.002-0.00260.0030.0122-0.0334-0.054-0.01360.01870.04580.0108-0.01840.02610.107-0.0128-0.01690.12140.16580.19046.351321.284278.8736
160.0009-0.00060.00120.0006-0.00230.00730.00580.00710.0053-0.008-0.0073-0.00390.01080.0220.00570.0958-0.02330.00720.1180.08120.104410.266630.070573.0373
170.01090.0042-0.00260.00680.00340.0066-0.0045-0.0570.0273-0.02110.0140.009-0.0244-0.0288-0.00310.15720.02910.01940.14490.06460.1619-1.187541.93178.3129
180-0.0003-0.00070.00240.0030.00480.00670.0022-0.0018-0.0180.00460.00080.0041-0.00280.00790.1127-0.0373-0.00350.14150.15970.17421.943131.230267.4492
190.0025-0.0010.00050.00580.0005-0.0002-0.01130.0131-0.0061-0.0082-0.0027-0.00060.0142-0.0008-0.00020.3968-0.00410.03490.28040.01150.40684.496914.699866.1533
200.0273-0.00460.01920.0021-0.0090.0685-0.0276-0.03140.01090.0052-0.035-0.0078-0.0168-0.0018-0.02810.0777-0.0223-0.02690.15020.09010.1833-18.17724.830184.2547
210.0376-0.02080.03390.0315-0.0160.0307-0.002-0.1253-0.03950.06210.0052-0.0018-0.0053-0.0188-0.00950.0933-0.0421-0.00580.15230.15880.1704-24.507232.969680.0785
220.01660.00610.00120.0101-0.00640.00710.0212-0.0095-0.0037-0.0214-0.0039-0.02340.0075-0.00840.02280.1305-0.02850.01610.11330.1330.1617-24.45636.571772.8014
230.014-0.005-0.00550.00270.00480.007-0.0183-0.0331-0.0424-0.00250.01490.02610.0023-0.0034-0.00690.0721-0.03080.00030.17880.16930.1842-34.825728.670977.1653
240.0118-0.009-0.01270.00940.01170.014-0.0361-0.0131-0.0582-0.0298-0.03470.0315-0.020.0007-0.00640.1585-0.0157-0.04780.17170.12880.3778-31.750719.858879.2817
250.0152-0.0158-0.01360.01840.01480.013-0.0808-0.0282-0.05350.0567-0.0049-0.01350.05160.0353-0.00020.1473-0.01850.00120.1480.10290.3099-23.500416.464879.3472
260.0014-0.00020.0009-0.0001-0.00070.00080.0095-0.0050.0051-0.02050.0054-0.0044-0.01250.00230.00020.31-0.0074-0.03160.3850.02970.3371-27.89429.515360.4769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 40 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 63 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 111 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 137 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 150 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid -2 through 17 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 63 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 76 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 77 through 101 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 102 through 111 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 112 through 137 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 150 )B0
13X-RAY DIFFRACTION13chain 'C' and (resid -2 through 40 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 41 through 63 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 64 through 94 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 95 through 110 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 111 through 126 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 127 through 137 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 138 through 149 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid -1 through 17 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 18 through 63 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 64 through 76 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 77 through 94 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 95 through 116 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 117 through 137 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 138 through 149 )D0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more