[English] 日本語
Yorodumi
- PDB-6fnn: Caldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fnn
TitleCaldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex
Components
  • 26S proteasome regulatory subunit N11-like protein
  • Ubiquitin-like protein
KeywordsHYDROLASE / deubiquitination / deubiquitylation / JAMM protease
Function / homology
Function and homology information


polyubiquitin modification-dependent protein binding / proteasome complex / metallopeptidase activity / ubiquitin-dependent protein catabolic process / metal ion binding / cytosol
Similarity search - Function
: / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. ...: / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like protein / 26S proteasome regulatory subunit N11-like protein
Similarity search - Component
Biological speciesCandidatus Caldiarchaeum subterraneum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFuchs, A.C.D. / Albrecht, R. / Martin, J. / Hartmann, M.D.
CitationJournal: Nat Commun / Year: 2018
Title: Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system.
Authors: Fuchs, A.C.D. / Maldoner, L. / Wojtynek, M. / Hartmann, M.D. / Martin, J.
History
DepositionFeb 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 26S proteasome regulatory subunit N11-like protein
B: 26S proteasome regulatory subunit N11-like protein
C: Ubiquitin-like protein
D: Ubiquitin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1778
Polymers56,8544
Non-polymers3234
Water6,630368
1
A: 26S proteasome regulatory subunit N11-like protein
C: Ubiquitin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5884
Polymers28,4272
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-80 kcal/mol
Surface area12060 Å2
MethodPISA
2
B: 26S proteasome regulatory subunit N11-like protein
D: Ubiquitin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5884
Polymers28,4272
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-60 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.674, 94.571, 170.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein 26S proteasome regulatory subunit N11-like protein


Mass: 17061.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Caldiarchaeum subterraneum (archaea)
Gene: CSUB_C1473, HGMM_F04B03C04, HGMM_F21D07C20, HGMM_F30C12C32
Production host: Escherichia coli (E. coli) / References: UniProt: E6N8B9, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin-like protein


Mass: 11365.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Caldiarchaeum subterraneum (archaea)
Gene: CSUB_C1474, HGMM_F04B03C03, HGMM_F21D07C21, HGMM_F30C12C33
Production host: Escherichia coli (E. coli) / References: UniProt: E6N8B8
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate, pH 4.6, 1.5 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.283 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.85→37.9 Å / Num. obs: 58917 / % possible obs: 99.6 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.8
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.66 / Num. unique obs: 9241 / CC1/2: 0.9 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FJV

6fjv


Resolution: 1.85→37.9 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.949 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20058 2946 5 %RANDOM
Rwork0.17269 ---
obs0.17409 55970 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å2-0 Å2
2---1.78 Å20 Å2
3---2.24 Å2
Refinement stepCycle: 1 / Resolution: 1.85→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3631 0 12 368 4011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193792
X-RAY DIFFRACTIONr_bond_other_d0.0010.023758
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9855164
X-RAY DIFFRACTIONr_angle_other_deg0.72438660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8955500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82523.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34915649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1171520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214236
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02782
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_it1.3722.3051970
X-RAY DIFFRACTIONr_mcbond_other1.3732.3051969
X-RAY DIFFRACTIONr_mcangle_it2.0913.4472465
X-RAY DIFFRACTIONr_mcangle_other2.0923.4472466
X-RAY DIFFRACTIONr_scbond_it2.1462.6041822
X-RAY DIFFRACTIONr_scbond_other2.1462.6041822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4083.7822694
X-RAY DIFFRACTIONr_long_range_B_refined7.61920.6034511
X-RAY DIFFRACTIONr_long_range_B_other7.44319.4844324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.846→1.894 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 206 -
Rwork0.398 3928 -
obs--95.69 %
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)
12.39751.2441-0.42342.8683-0.12774.69940.01720.12180.1177-0.03680.0210.1841-0.0018-0.2314-0.03820.0544-0.03950.00710.0481-0.00220.01426.730828.484912.7255
23.2910.1505-1.35372.78531.05113.06590.08730.13910.23020.00120.00010.2379-0.1012-0.187-0.08750.0869-0.07620.00710.09880.01580.0382-14.844111.854720.8901
38.62822.3988-0.1610.7905-3.415810.03530.0401-0.17880.41280.5159-0.0649-0.4344-1.13590.08280.02470.22640.0684-0.0180.1719-0.09920.187748.605535.2365-2.7435
47.38451.3352-0.97476.0765-6.163313.0183-0.17440.60730.0051-0.50930.26340.287-0.1823-0.2025-0.0890.24060.0847-0.00790.19460.02980.1999-33.674-22.732550.0527
55.43392.00680.02283.23790.82862.45260.020.1108-0.41220.05050.1196-0.43380.17520.3831-0.13960.104-0.0420.00590.1169-0.03670.066630.700531.942411.5583
63.40822.3982-0.49374.9929-0.86943.12110.3164-0.4894-0.28740.7726-0.3388-0.34130.03940.13980.02240.2669-0.1492-0.01560.1644-0.00120.0666-22.8497-6.145135.604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 148
2X-RAY DIFFRACTION2B-3 - 148
3X-RAY DIFFRACTION3C-11 - 0
4X-RAY DIFFRACTION4D-11 - 0
5X-RAY DIFFRACTION5C1 - 78
6X-RAY DIFFRACTION6D1 - 78

+
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