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- PDB-6czk: Crystal structure of wild-type human pro-cathepsin H -

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Basic information

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


cathepsin H / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / immune response-regulating signaling pathway / positive regulation of peptidase activity / multivesicular body lumen / alveolar lamellar body / membrane protein proteolysis / bradykinin catabolic process ...cathepsin H / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / immune response-regulating signaling pathway / 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 / MHC class II antigen presentation / ERK1 and ERK2 cascade / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_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)39,44510
Polymers37,4501
Non-polymers1,9969
Water5,999333
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)97.416, 97.416, 107.530
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-527-

HOH

21A-764-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pro-cathepsin H


Mass: 37449.559 Da / Num. of mol.: 1
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 , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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

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Non-polymers , 3 types, 340 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 3.93 Å3/Da / Density % sol: 68.73 %
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: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 40304 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.087 / Χ2: 1.054 / Net I/σ(I): 13
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 1973 / Rpim(I) all: 0.202 / Rrim(I) all: 0.553 / Χ2: 0.937 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8PCH

8pch


Resolution: 2.001→44.368 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 18.38
RfactorNum. reflection% reflection
Rfree0.1996 1981 4.98 %
Rwork0.1705 --
obs0.172 39803 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→44.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 127 333 2930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082708
X-RAY DIFFRACTIONf_angle_d0.9223684
X-RAY DIFFRACTIONf_dihedral_angle_d11.9471576
X-RAY DIFFRACTIONf_chiral_restr0.054389
X-RAY DIFFRACTIONf_plane_restr0.006456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0005-2.05050.23021320.20952535X-RAY DIFFRACTION95
2.0505-2.1060.24541350.19482631X-RAY DIFFRACTION96
2.106-2.16790.21511430.18512638X-RAY DIFFRACTION98
2.1679-2.23790.20881350.17472633X-RAY DIFFRACTION98
2.2379-2.31790.17621400.17192673X-RAY DIFFRACTION99
2.3179-2.41070.19951450.17622702X-RAY DIFFRACTION99
2.4107-2.52040.19921350.17882682X-RAY DIFFRACTION100
2.5204-2.65330.22651430.18812710X-RAY DIFFRACTION99
2.6533-2.81950.22881450.18832720X-RAY DIFFRACTION100
2.8195-3.03710.26081440.18262733X-RAY DIFFRACTION100
3.0371-3.34270.21551410.17462742X-RAY DIFFRACTION100
3.3427-3.82610.17081470.14942756X-RAY DIFFRACTION100
3.8261-4.81960.15541430.13512784X-RAY DIFFRACTION100
4.8196-44.37930.19541530.17992883X-RAY DIFFRACTION100

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