[English] 日本語
Yorodumi
- PDB-3f75: Activated Toxoplasma gondii cathepsin L (TgCPL) in complex with i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f75
TitleActivated Toxoplasma gondii cathepsin L (TgCPL) in complex with its propeptide
Components
  • Cathepsin L Propeptide
  • Cathepsin L Protease
KeywordsHYDROLASE / MEDICAL STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA / MSGPP / cysteine protease / parasite / protozoa / Thiol protease
Function / homology
Function and homology information


cysteine-type peptidase activity / membrane => GO:0016020
Similarity search - Function
Helix Hairpins - #2250 / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Helix Hairpins - #2250 / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Helix Hairpins / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Cathepsin L
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Toxoplasma gondii cathepsin L is the primary target of the invasion-inhibitory compound morpholinurea-leucyl-homophenyl-vinyl sulfone phenyl.
Authors: Larson, E.T. / Parussini, F. / Huynh, M.H. / Giebel, J.D. / Kelley, A.M. / Zhang, L. / Bogyo, M. / Merritt, E.A. / Carruthers, V.B.
History
DepositionNov 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Jul 31, 2013Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cathepsin L Protease
P: Cathepsin L Propeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4366
Polymers37,2232
Non-polymers2134
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-13.9 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.621, 65.621, 149.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-481-

HOH

-
Components

-
Protein , 2 types, 2 molecules AP

#1: Protein Cathepsin L Protease / Toxopain-2


Mass: 24428.521 Da / Num. of mol.: 1 / Fragment: UNP residues 199-422
Source method: isolated from a genetically manipulated source
Details: expressed together with chain P as procathepsin L and autoactivated but propeptide not purified from active protease prior to crystallization; structure is a complex of the active protease ...Details: expressed together with chain P as procathepsin L and autoactivated but propeptide not purified from active protease prior to crystallization; structure is a complex of the active protease and its propeptide, labeled as chain A and chain P, respectively, to indicate that they are distinct polypeptide chains
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: CPL / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q6DMN0, cathepsin L
#2: Protein Cathepsin L Propeptide / Toxopain-2


Mass: 12794.354 Da / Num. of mol.: 1 / Fragment: UNP residues 105-198
Mutation: N-terminal His tag replaced all but the last 94 residues of the propeptide domain
Source method: isolated from a genetically manipulated source
Details: N-terminal His tag replaced all but the last 94 residues of the propeptide domain; expressed together with chain A as procathepsin L and autoactivated but propeptide not purified from active ...Details: N-terminal His tag replaced all but the last 94 residues of the propeptide domain; expressed together with chain A as procathepsin L and autoactivated but propeptide not purified from active protease prior to crystallization; structure is a complex of the active protease and its propeptide, labeled as chain A and chain P, respectively, to indicate that they are distinct polypeptide chains
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: CPL / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q6DMN0, cathepsin L

-
Non-polymers , 4 types, 169 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence details1. THE TARGETDB ID FOR THIS PROTEIN WAS NOT AVAILABLE AT THE TIME OF DEPOSITION. 2. THIS ENTRY IS A ...1. THE TARGETDB ID FOR THIS PROTEIN WAS NOT AVAILABLE AT THE TIME OF DEPOSITION. 2. THIS ENTRY IS A COMPLEX OF THE ACTIVE PROTEASE AND ITS PROPEPTIDE, LABELED AS CHAIN A AND CHAIN P, RESPECTIVELY, TO INDICATE THAT THEY ARE DISTINCT POLYPEPTIDE CHAINS. 3. ENTITY 1 (CHAIN A): EXPRESSED TOGETHER WITH CHAIN P AS PROCATHEPSIN L AND AUTOACTIVATED, BUT PROPEPTIDE NOT PURIFIED FROM ACTIVE PROTEASE PRIOR TO CRYSTALLIZATION. 4. ENTITY 2 (CHAIN P): N-TERMINAL HIS TAG REPLACED ALL BUT THE LAST 94 RESIDUES OF THE PROPEPTIDE DOMAIN. EXPRESSED TOGETHER WITH CHAIN A AS PROCATHEPSIN L AND AUTOACTIVATED, BUT PROPEPTIDE NOT PURIFIED FROM ACTIVE PROTEASE PRIOR TO CRYSTALLIZATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 40% PEG 8000, 0.1M Ammonium bromide, 0.1M Sodium citrate pH 4.0. Cryoprotected with ~10% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2008
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. all: 23266 / Num. obs: 23266 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.122 / Χ2: 1.026 / Net I/σ(I): 18.128
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2242 / Χ2: 1.031 / % possible all: 99.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.41 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.99 Å
Translation2.5 Å33.99 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.5.0047refinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CS8 (protease domain only)

1cs8


Resolution: 1.99→33.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 7.38 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20557 1186 5.1 %RANDOM
Rwork0.16538 ---
obs0.16739 23178 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.904 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.43 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.99→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 7 165 2517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212433
X-RAY DIFFRACTIONr_bond_other_d0.0010.021697
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9393272
X-RAY DIFFRACTIONr_angle_other_deg1.1873.0044094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5425298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75224.016122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77215420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7571515
X-RAY DIFFRACTIONr_chiral_restr0.070.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
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_it1.69541478
X-RAY DIFFRACTIONr_mcbond_other0.5414615
X-RAY DIFFRACTIONr_mcangle_it2.58162347
X-RAY DIFFRACTIONr_scbond_it3.2996955
X-RAY DIFFRACTIONr_scangle_it4.95810925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 88 -
Rwork0.22 1563 -
all0.224 1659 -
obs-1651 99.52 %
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)
15.0141.59761.35420.69990.22085.0691-0.0945-0.50170.56220.19-0.1610.1737-0.4786-0.15120.25550.26190.0389-0.01380.1317-0.02120.091730.85110.38960.653
21.05260.1041-0.13361.3822-0.01571.54530.03240.02460.0664-0.00760.0210.304-0.073-0.3475-0.05350.02150.05420.00010.16220.01320.118115.73414.43439.828
36.592-1.8504-0.1472.75291.41733.1360.1644-0.1850.6250.1134-0.17250.0124-0.2436-0.07310.0080.14880.0360.03090.1369-0.03420.099430.08921.07855.67
40.72210.1182-0.2211.1040.01261.271-0.0062-0.0874-0.00040.0968-0.0102-0.0264-0.04170.02690.01640.07520.0254-0.00280.109-0.00320.087835.99913.12344.892
511.2111.3313-3.31026.1258-0.35055.1838-0.0013-0.2859-0.1586-0.0530.0052-0.84920.1250.7099-0.00390.15340.0367-0.01730.1255-0.01230.12244.436-1.03319.43
62.3824-0.69440.23520.9804-0.64455.29340.04010.19070.02960.0164-0.0876-0.1766-0.13390.31210.04750.0967-0.0088-0.02460.1008-0.00240.053135.2126.99514.27
71.191-0.16181.23360.8015-0.46494.0785-0.04080.0644-0.0524-0.03930.0181-0.10150.01350.2810.02270.08630.01070.00090.115-0.00540.070544.9526.78329.212
84.8934-1.0971-3.05073.81760.87323.8077-0.01950.0190.209-0.15730.10670.2228-0.3245-0.2929-0.08720.07270.0325-0.03860.12460.01890.080832.37819.5629.243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 15
2X-RAY DIFFRACTION2A16 - 118
3X-RAY DIFFRACTION3A119 - 135
4X-RAY DIFFRACTION4A136 - 224
5X-RAY DIFFRACTION5P108 - 123
6X-RAY DIFFRACTION6P124 - 136
7X-RAY DIFFRACTION7P137 - 168
8X-RAY DIFFRACTION8P169 - 182

+
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