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- PDB-6czs: Crystal structure of human pro-cathepsin H C26S mutant -

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Basic information

Entry
Database: PDB / ID: 6czs
TitleCrystal structure of human pro-cathepsin H C26S mutant
ComponentsPro-cathepsin H
KeywordsHYDROLASE / papain family cysteine peptidase / protein degradation in lysosome / inhibitory prodomain
Function / homology
Function and homology information


cathepsin H / immune response-regulating signaling pathway / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / positive regulation of peptidase activity / multivesicular body lumen / alveolar lamellar body / membrane protein proteolysis / bradykinin catabolic process ...cathepsin H / immune response-regulating signaling pathway / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / positive regulation of peptidase activity / multivesicular body lumen / alveolar lamellar body / membrane protein proteolysis / bradykinin catabolic process / Surfactant metabolism / metanephros development / surfactant homeostasis / cellular response to thyroid hormone stimulus / zymogen activation / positive regulation of epithelial cell migration / thyroid hormone binding / antigen processing and presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / aminopeptidase activity / response to retinoic acid / cysteine-type peptidase activity / ERK1 and ERK2 cascade / MHC class II antigen presentation / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / protein destabilization / T cell mediated cytotoxicity / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / tertiary granule lumen / peptidase activity / secretory granule lumen / collagen-containing extracellular matrix / adaptive immune response / endopeptidase activity / ficolin-1-rich granule lumen / lysosome / positive regulation of cell migration / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / extracellular region / cytosol
Similarity search - Function
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 ...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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
trehalose / Pro-cathepsin H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsHuang, X. / Hao, Y.
CitationJournal: PLoS ONE / Year: 2018
Title: Crystal structures of human procathepsin H.
Authors: Hao, Y. / Purtha, W. / Cortesio, C. / Rui, H. / Gu, Y. / Chen, H. / Sickmier, E.A. / Manzanillo, P. / Huang, X.
History
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pro-cathepsin H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,78512
Polymers37,4171
Non-polymers2,36811
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.242, 98.242, 106.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-776-

HOH

21A-850-

HOH

31A-904-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pro-cathepsin H


Mass: 37417.492 Da / Num. of mol.: 1 / Mutation: C26S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSH, CPSB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P09668, cathepsin H

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 505 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M sodium phosphate dibasic / citric acid, pH 4.2, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→49.12 Å / Num. obs: 70589 / % possible obs: 100 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.02 / Rrim(I) all: 0.089 / Net I/σ(I): 20.4
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 20.4 % / Rmerge(I) obs: 1.658 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3478 / Rpim(I) all: 0.376 / Rrim(I) all: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8PCH

8pch


Resolution: 1.66→49.121 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 3425 4.86 %
Rwork0.1813 --
obs0.1825 70456 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→49.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 148 498 3115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072756
X-RAY DIFFRACTIONf_angle_d0.9033763
X-RAY DIFFRACTIONf_dihedral_angle_d10.6861592
X-RAY DIFFRACTIONf_chiral_restr0.052407
X-RAY DIFFRACTIONf_plane_restr0.006464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.68370.31061390.28062759X-RAY DIFFRACTION100
1.6837-1.70890.32511750.26842719X-RAY DIFFRACTION100
1.7089-1.73560.26811590.26482747X-RAY DIFFRACTION100
1.7356-1.7640.28231350.2352782X-RAY DIFFRACTION100
1.764-1.79440.24231500.22872762X-RAY DIFFRACTION100
1.7944-1.82710.24571480.21122765X-RAY DIFFRACTION100
1.8271-1.86220.23161440.21722762X-RAY DIFFRACTION100
1.8622-1.90020.28131580.25842737X-RAY DIFFRACTION99
1.9002-1.94160.33161140.29122781X-RAY DIFFRACTION100
1.9416-1.98670.23311180.20282828X-RAY DIFFRACTION100
1.9867-2.03640.22031630.19562746X-RAY DIFFRACTION100
2.0364-2.09150.22641400.19592801X-RAY DIFFRACTION100
2.0915-2.1530.23081350.19262773X-RAY DIFFRACTION100
2.153-2.22250.20751330.19442759X-RAY DIFFRACTION99
2.2225-2.30190.25171620.22022768X-RAY DIFFRACTION99
2.3019-2.39410.16741400.17232770X-RAY DIFFRACTION100
2.3941-2.50310.18221530.17052779X-RAY DIFFRACTION100
2.5031-2.6350.20161300.1712815X-RAY DIFFRACTION100
2.635-2.80010.21851520.17232800X-RAY DIFFRACTION100
2.8001-3.01630.19441430.16682800X-RAY DIFFRACTION100
3.0163-3.31970.17021260.16482845X-RAY DIFFRACTION100
3.3197-3.80.16471300.14132865X-RAY DIFFRACTION100
3.8-4.78690.1531310.12312873X-RAY DIFFRACTION100
4.7869-49.14250.20051470.17012995X-RAY DIFFRACTION100

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