[English] 日本語
Yorodumi
- PDB-2wzn: 3d structure of TET3 from Pyrococcus horikoshii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wzn
Title3d structure of TET3 from Pyrococcus horikoshii
Components354AA LONG HYPOTHETICAL OPERON PROTEIN FRV
KeywordsHYDROLASE / PROTEASE / THERMOPHILIC / SELF-COMPARTMENTALISING
Function / homology
Function and homology information


aminopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / Peptidase M42, domain 2 / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
354aa long hypothetical operon protein Frv
Similarity search - Component
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRosenbaum, E. / Dura, M.A. / Vellieux, F.M. / Franzetti, B.
Citation
Journal: Mol.Microbiol. / Year: 2009
Title: The Structural and Biochemical Characterizations of a Novel Tet Peptidase Complex from Pyrococcus Horikoshii Reveal an Integrated Peptide Degradation System in Hyperthermophilic Archaea.
Authors: Dura, M.A. / Rosenbaum, E. / Larabi, A. / Gabel, F. / Vellieux, F.M. / Franzetti, B.
#1: Journal: J Biol Chem / Year: 2006
Title: An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron.
Authors: Guy Schoehn / Frédéric M D Vellieux / M Asunción Durá / Véronique Receveur-Bréchot / Céline M S Fabry / Rob W H Ruigrok / Christine Ebel / Alain Roussel / Bruno Franzetti /
Abstract: Cellular proteolysis involves large oligomeric peptidases that play key roles in the regulation of many cellular processes. The cobalt-activated peptidase TET1 from the hyperthermophilic Archaea ...Cellular proteolysis involves large oligomeric peptidases that play key roles in the regulation of many cellular processes. The cobalt-activated peptidase TET1 from the hyperthermophilic Archaea Pyrococcus horikoshii (PhTET1) was found to assemble as a 12-subunit tetrahedron and as a 24-subunit octahedral particle. Both quaternary structures were solved by combining x-ray crystallography and cryoelectron microscopy data. The internal organization of the PhTET1 particles reveals highly self-compartmentalized systems made of networks of access channels extended by vast catalytic chambers. The two edifices display aminopeptidase activity, and their organizations indicate substrate navigation mechanisms different from those described in other large peptidase complexes. Compared with the tetrahedron, the octahedron forms a more expanded hollow structure, representing a new type of giant peptidase complex. PhTET1 assembles into two different quaternary structures because of quasi-equivalent contacts that previously have only been identified in viral capsids.
History
DepositionDec 1, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionNov 3, 2010ID: 2VPU
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 354AA LONG HYPOTHETICAL OPERON PROTEIN FRV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4177
Polymers39,0311
Non-polymers3866
Water3,891216
1
A: 354AA LONG HYPOTHETICAL OPERON PROTEIN FRV
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)473,00084
Polymers468,36912
Non-polymers4,63172
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation8_555-z,x,-y1
Buried area64280 Å2
ΔGint-1465.7 kcal/mol
Surface area122050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.241, 132.241, 132.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-2075-

HOH

-
Components

#1: Protein 354AA LONG HYPOTHETICAL OPERON PROTEIN FRV / TET3


Mass: 39030.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: O59485
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.36 Å3/Da / Density % sol: 47.37 % / Description: DATA WERE COLLECTED USING THE ROTATION METHOD
Crystal growpH: 8.5
Details: 0.17 M AMMONIUM SULPHATE, 0.085 M TRIS HCL PH 8.5, 21.25% (W/V) PEG 3300, 2.0 MICROL DROPLETS TO WHICH 0.5 MICROL OF 30% GAMMA-BUTYROLACTONE IS ADDED

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 7, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→33 Å / Num. obs: 433624 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 14.5 % / Biso Wilson estimate: 29.22 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18
Reflection shellResolution: 1.9→2.1 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 7 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y0Y

1y0y


Resolution: 1.9→29.57 Å / SU ML: 0.2 / σ(F): 1.37 / Phase error: 16.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1752 1518 5 %
Rwork0.1471 --
obs0.1485 30368 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.22 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso mean: 33.06 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 16 216 2847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072704
X-RAY DIFFRACTIONf_angle_d1.1173668
X-RAY DIFFRACTIONf_dihedral_angle_d16.0691014
X-RAY DIFFRACTIONf_chiral_restr0.082415
X-RAY DIFFRACTIONf_plane_restr0.004481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.20421510.17692853X-RAY DIFFRACTION100
1.9679-2.04670.20181500.16042864X-RAY DIFFRACTION100
2.0467-2.13980.21291500.14422834X-RAY DIFFRACTION100
2.1398-2.25260.19381510.1492877X-RAY DIFFRACTION100
2.2526-2.39370.19231510.15042867X-RAY DIFFRACTION100
2.3937-2.57840.19171520.152871X-RAY DIFFRACTION100
2.5784-2.83770.18631520.14732901X-RAY DIFFRACTION100
2.8377-3.24790.1811520.14532889X-RAY DIFFRACTION100
3.2479-4.09030.16451540.12652915X-RAY DIFFRACTION100
4.0903-29.57360.14231550.14672979X-RAY DIFFRACTION100
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)
11.1310.6833-0.09950.6329-0.11230.02280.2487-0.34130.08320.0961-0.2175-0.0057-0.02950.08180.00460.336-0.03190.02910.3334-0.02460.2415-7.689914.187747.5249
20.42470.33460.16861.1423-0.24920.28980.0734-0.1715-0.00640.1966-0.03330.0897-0.0247-0.0436-0.02380.21760.01040.04590.2516-0.02350.1919-16.381111.161841.1602
32.0293-0.6573-0.71121.1599-0.29471.1680.10250.0076-0.3987-0.3752-0.12870.04490.33670.02250.00960.30050.00280.02120.2254-0.00080.2528-11.6507-9.38132.1128
40.3358-0.22540.15580.8106-0.00590.14980.0458-0.090.06570.0874-0.0691-0.0117-0.072-0.04550.01890.25410.01060.0330.2354-0.02980.1858-7.86920.82339.3388
51.2153-0.6516-0.03890.647-0.43060.6888-0.01730.0780.26920.0512-0.0655-0.1866-0.1257-0.01160.070.2723-0.0120.00460.2172-0.03820.272-2.352535.215534.307
60.5760.0124-0.20860.1392-0.06220.60680.0225-0.11330.146-0.0029-0.0214-0.0036-0.1921-0.0681-0.01580.25110.00840.02110.2076-0.06720.2221-7.432928.631437.1178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 8:28)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 29:115)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 116:160)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 161:256)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 257:293)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 294:354)

+
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