[English] 日本語
Yorodumi
- PDB-1ef7: CRYSTAL STRUCTURE OF HUMAN CATHEPSIN X -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ef7
TitleCRYSTAL STRUCTURE OF HUMAN CATHEPSIN X
ComponentsCATHEPSIN X
KeywordsHYDROLASE / papain-like / cysteine protease / carboxypeptidase / cathepsin
Function / homology
Function and homology information


cathepsin X / negative regulation of plasminogen activation / Cargo concentration in the ER / COPII-mediated vesicle transport / Lysosome Vesicle Biogenesis / epithelial tube branching involved in lung morphogenesis / COPII-coated ER to Golgi transport vesicle / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity ...cathepsin X / negative regulation of plasminogen activation / Cargo concentration in the ER / COPII-mediated vesicle transport / Lysosome Vesicle Biogenesis / epithelial tube branching involved in lung morphogenesis / COPII-coated ER to Golgi transport vesicle / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / cysteine-type peptidase activity / endoplasmic reticulum-Golgi intermediate compartment membrane / proteolysis involved in protein catabolic process / specific granule lumen / cell cortex / cytoplasmic vesicle / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / lysosome / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Cathepsin Z / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily ...Cathepsin Z / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.67 Å
AuthorsGuncar, G. / Klemencic, I. / Turk, B. / Turk, V. / Karaoglanovic-Carmona, A. / Juliano, L. / Turk, D.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of cathepsin X: a flip-flop of the ring of His23 allows carboxy-monopeptidase and carboxy-dipeptidase activity of the protease.
Authors: Guncar, G. / Klemencic, I. / Turk, B. / Turk, V. / Karaoglanovic-Carmona, A. / Juliano, L. / Turk, D.
History
DepositionFeb 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CATHEPSIN X
B: CATHEPSIN X


Theoretical massNumber of molelcules
Total (without water)54,3542
Polymers54,3542
Non-polymers00
Water2,126118
1
A: CATHEPSIN X


Theoretical massNumber of molelcules
Total (without water)27,1771
Polymers27,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CATHEPSIN X


Theoretical massNumber of molelcules
Total (without water)27,1771
Polymers27,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: CATHEPSIN X

B: CATHEPSIN X


Theoretical massNumber of molelcules
Total (without water)54,3542
Polymers54,3542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x+1/2,y+1/2,z1
Buried area3720 Å2
ΔGint-20 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.251, 92.480, 209.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a monomer.

-
Components

#1: Protein CATHEPSIN X /


Mass: 27177.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: LIVER / References: UniProt: Q9UBR2, cathepsin X
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, 2-propanol, Na-HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.8 mg/mlprotein1drop
220 mMNa acetate1drop
31 mMEDTA1drop
414.4 %PEG40001reservoir
57.2 %2-propanol1reservoir
60.072 MNa-HEPES1reservoir

-
Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.67→13.4 Å / Num. all: 16880 / Num. obs: 16732 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 9.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.9
Reflection shellResolution: 2.67→2.83 Å / Rmerge(I) obs: 0.24 / Num. unique all: 2181
Reflection
*PLUS
Num. measured all: 152861
Reflection shell
*PLUS
% possible obs: 87 % / Mean I/σ(I) obs: 3.6

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
MAINrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2.67→10 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.226 1346 random 12
obs0.183 16433 -
Refinement stepCycle: LAST / Resolution: 2.67→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 0 118 3934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
Software
*PLUS
Name: MAIN / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 25.3
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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