[English] 日本語
Yorodumi
- PDB-3kfq: Unreduced cathepsin V in complex with stefin A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kfq
TitleUnreduced cathepsin V in complex with stefin A
Components
  • Cathepsin L2
  • Cystatin-A
KeywordsHydrolase/Hydrolase inhibitor / papain-like cysteine protease / cathepsin / protease-inhibitor complex / Hydrolase / Lysosome / Protease / Thiol protease / Zymogen / Protease inhibitor / Thiol protease inhibitor / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


cathepsin V / negative regulation of peptidase activity / peptidase inhibitor complex / Formation of the cornified envelope / peptide cross-linking / cornified envelope / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase inhibitor activity ...cathepsin V / negative regulation of peptidase activity / peptidase inhibitor complex / Formation of the cornified envelope / peptide cross-linking / cornified envelope / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase inhibitor activity / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / extracellular matrix disassembly / keratinocyte differentiation / cysteine-type peptidase activity / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / negative regulation of proteolysis / Endosomal/Vacuolar pathway / cell-cell adhesion / antigen processing and presentation of exogenous peptide antigen via MHC class II / protease binding / immune response / cysteine-type endopeptidase activity / serine-type endopeptidase activity / extracellular space / extracellular region / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) ...Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / 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 / Nuclear Transport Factor 2; Chain: A, / Papain-like cysteine peptidase superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cathepsin L2 / Cystatin-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsRenko, M. / Turk, D.
CitationJournal: To be Published
Title: Unreduced cathepsin V in complex with stefin A
Authors: Renko, M. / Turk, D.
History
DepositionOct 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cathepsin L2
B: Cathepsin L2
C: Cystatin-A
D: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)70,2154
Polymers70,2154
Non-polymers00
Water13,007722
1
A: Cathepsin L2
D: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)35,1082
Polymers35,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area14090 Å2
MethodPISA
2
B: Cathepsin L2
C: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)35,1082
Polymers35,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-12 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.313, 107.290, 115.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cathepsin L2 / / Cathepsin V / Cathepsin U


Mass: 24087.053 Da / Num. of mol.: 2 / Mutation: N108Q,N179D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: O60911, cathepsin V
#2: Protein Cystatin-A / Cystatin-AS / Stefin-A


Mass: 11020.464 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01040
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCATHEPSIN V WAS BLOCKED WITH MMTS (METHYL METHANETHIOSULFONATE), LEAVING -S-CH3 ATOMS ON ACTIVE ...CATHEPSIN V WAS BLOCKED WITH MMTS (METHYL METHANETHIOSULFONATE), LEAVING -S-CH3 ATOMS ON ACTIVE SITE CYSTEINE RESIDUE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.19 % / Mosaicity: 0.546 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris-HCl, 12% PEG3000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2008 / Details: Collimating and focusing, Pt-coated mirrors
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→22 Å / Num. all: 51300 / Num. obs: 51049 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.2 % / Rmerge(I) obs: 0.079 / Χ2: 0.88 / Net I/σ(I): 8
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.43 / Num. unique all: 2302 / Χ2: 0.462 / % possible all: 91.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h6s, 1nb3

3h6s

1nb3


Resolution: 1.99→19.49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.164 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.867 / SU R Cruickshank DPI: 0.166 / SU Rfree: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. The structure was refined also with MAIN
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2586 5.1 %RANDOM
Rwork0.176 ---
all0.182 51180 --
obs0.178 50986 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.22 Å2 / Biso mean: 32.922 Å2 / Biso min: 13.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å2-0 Å2-0 Å2
2---1.21 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.99→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 0 722 5654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225010
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9516783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5555634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79325.566221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57815832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2931512
X-RAY DIFFRACTIONr_chiral_restr0.1280.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213846
X-RAY DIFFRACTIONr_mcbond_it0.9161.53156
X-RAY DIFFRACTIONr_mcangle_it1.60725055
X-RAY DIFFRACTIONr_scbond_it2.61531854
X-RAY DIFFRACTIONr_scangle_it4.1234.51728
LS refinement shellResolution: 1.995→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 169 -
Rwork0.22 3443 -
all-3612 -
obs--96.97 %

+
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