[English] 日本語
Yorodumi
- PDB-1cpj: CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cpj
TitleCRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN
ComponentsCATHEPSIN B
KeywordsHYDROLASE / THIOL PROTEASE
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / kininogen binding / cathepsin B / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / response to kainic acid / thyroid hormone generation ...Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / kininogen binding / cathepsin B / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / response to kainic acid / thyroid hormone generation / cellular response to thyroid hormone stimulus / proteoglycan binding / Neutrophil degranulation / response to dexamethasone / response to amine / collagen catabolic process / decidualization / response to mechanical stimulus / response to glucose / skeletal muscle tissue development / collagen binding / response to cytokine / epithelial cell differentiation / peptide binding / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / protein catabolic process / sarcolemma / caveola / response to peptide hormone / autophagy / cellular response to mechanical stimulus / melanosome / peptidase activity / response to ethanol / spermatogenesis / neuron apoptotic process / endopeptidase activity / lysosome / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / symbiont entry into host cell / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsHuber, C.P. / Jia, Z.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex. Implications for structure-based inhibitor design.
Authors: Jia, Z. / Hasnain, S. / Hirama, T. / Lee, X. / Mort, J.S. / To, R. / Huber, C.P.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Crystallization of Recombinant Rat Cathepsin B
Authors: Lee, X. / Ahmed, F.R. / Hirama, T. / Huber, C.P. / Rose, D.R. / To, R. / Hasnain, S. / Tam, A. / Mort, J.S.
History
DepositionJul 17, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET THERE IS A BIFURCATED SHEET IN EACH MOLECULE. EACH IS REPRESENTED BY TWO SHEETS WITH SOME ...SHEET THERE IS A BIFURCATED SHEET IN EACH MOLECULE. EACH IS REPRESENTED BY TWO SHEETS WITH SOME STRANDS IN COMMON. THUS STRANDS 4, 5, 6 OF SHEETS SA1 AND SA2 ARE IDENTICAL TO STRANDS 2, 3, 4 OF SHEETS SA2 AND SB2 IN CHAINS A AND B, RESPECTIVELY.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CATHEPSIN B
B: CATHEPSIN B


Theoretical massNumber of molelcules
Total (without water)56,8832
Polymers56,8832
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.090, 90.250, 62.100
Angle α, β, γ (deg.)90.00, 97.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6338, 0.7386, 0.2297), (0.7394, -0.6657, 0.1002), (0.2269, 0.1064, -0.9681)
Vector: -52.751, 88.132, 93.844)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 253 B 1 .. B 253 0.457

-
Components

#1: Protein CATHEPSIN B


Mass: 28441.562 Da / Num. of mol.: 2 / Mutation: S115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CDNA / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00787, cathepsin B
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE V223A SUBSTITUTION WAS PRESENT IN THE PLASMID SUPPLIED TO DR. J. S. MORT BY DR. SHU CHAN ...THE V223A SUBSTITUTION WAS PRESENT IN THE PLASMID SUPPLIED TO DR. J. S. MORT BY DR. SHU CHAN ALTHOUGH IT IS NOT MENTIONED IN THE PAPER GIVING THE CDNA SEQUENCE. IT IS POSSIBLE THAT THIS CHANGE, ALSO WITH RESPECT TO THE ORIGINAL PROTEIN SEQUENCE FROM A PREPARATION OF PURIFIED PROTEIN, COULD REPRESENT A POLYMORPHISM BETWEEN THE STRAINS OF RAT THAT WERE USED IN EACH CASE. THE SUBSTITUTION IS NOT STRUCTURALLY IMPORTANT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.25 mg/mlcathepsin B1drop
23.27 mg/mlsynthetic propeptide1drop
320.5 %ammonium sulfate1reservoir
40.1 Msodium acetate1reservoir
51 %PEG40001reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 24886 / % possible obs: 90.7 % / Rmerge(I) obs: 0.095

-
Processing

Software
NameVersionClassification
SDMSdata collection
X-PLOR3model building
X-PLOR3refinement
SDMSdata reduction
X-PLOR3phasing
RefinementResolution: 2.2→8 Å / σ(F): 2
Details: RESIDUE ASN 222 OF BOTH CHAINS HAS PHI-PSI ANGLES OUTSIDE THE NORMALLY PERMITTED RANGE BECAUSE ITS SIDE CHAIN OXYGEN ATOM IS INVOLVED IN A HYDROGEN BOND WITH THE ADJACENT MAIN-CHAIN N-H 223.
RfactorNum. reflection% reflection
Rwork0.175 --
obs0.175 23373 93.9 %
Displacement parametersBiso mean: 21.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 0 190 4058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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