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- PDB-4n6n: Crystal structure of oxidized legumain in complex with cystatin E/M -

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Basic information

Entry
Database: PDB / ID: 4n6n
TitleCrystal structure of oxidized legumain in complex with cystatin E/M
Components
  • Cystatin-M
  • Legumain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / complex / cysteine protease / inhibitor / legumain / asparaginyl endopeptidase / reactive center loop / papain / cathepsin / cancer / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / cornified envelope / receptor catabolic process / vitamin D metabolic process / endolysosome lumen / response to acidic pH ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / cornified envelope / receptor catabolic process / vitamin D metabolic process / endolysosome lumen / response to acidic pH / positive regulation of monocyte chemotaxis / dendritic spine organization / Trafficking and processing of endosomal TLR / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / anatomical structure morphogenesis / cysteine-type endopeptidase inhibitor activity / epidermis development / endopeptidase activator activity / MHC class II antigen presentation / positive regulation of mitotic cell cycle / lysosomal lumen / cellular response to calcium ion / proteolysis involved in protein catabolic process / protein maturation / positive regulation of long-term synaptic potentiation / antigen processing and presentation of exogenous peptide antigen via MHC class II / tau protein binding / memory / cellular response to amyloid-beta / apical part of cell / late endosome / peptidase activity / negative regulation of neuron apoptotic process / lysosome / negative regulation of gene expression / cysteine-type endopeptidase activity / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Asparaginyl endopeptidase / Legumain prodomain superfamily / : / Legumain, prodomain / Peptidase C13, legumain / Peptidase C13 family / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain ...Asparaginyl endopeptidase / Legumain prodomain superfamily / : / Legumain, prodomain / Peptidase C13, legumain / Peptidase C13 family / 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 / Rossmann fold - #1460 / Nuclear Transport Factor 2; Chain: A, / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Cystatin-M / Legumain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsDall, E. / Brandstetter, H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Structure and mechanism of an aspartimide-dependent Peptide ligase in human legumain.
Authors: Dall, E. / Fegg, J.C. / Briza, P. / Brandstetter, H.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Legumain
B: Cystatin-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2609
Polymers46,6152
Non-polymers1,6457
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.610, 85.750, 58.950
Angle α, β, γ (deg.)90.00, 94.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Legumain / Asparaginyl endopeptidase / Protease / cysteine 1


Mass: 31689.641 Da / Num. of mol.: 1 / Fragment: UNP residues 26-303 / Mutation: N263Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGMN, PRSC1 / Production host: Leishmania tarentolae (eukaryote) / Strain (production host): P10 / References: UniProt: Q99538, legumain
#2: Protein Cystatin-M / Cystatin-6 / Cystatin-E


Mass: 14924.931 Da / Num. of mol.: 1 / Fragment: UNP residues 29-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CST6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15828

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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

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Non-polymers , 2 types, 249 molecules

#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES 147 AND 148 STARTED OUT AS ASP AND HIS. THE SIDECHAIN OF ASP ATTACKS THE FOLLOWING AMIDE ...RESIDUES 147 AND 148 STARTED OUT AS ASP AND HIS. THE SIDECHAIN OF ASP ATTACKS THE FOLLOWING AMIDE OF HIS TO FORM A SUCCINIMIDE RESIDUE SNN.

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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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 4000, 100 mM MES pH 6.5, 200 mM potassium iodide, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.87→48.47 Å / Num. obs: 35804 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.87→1.97 Å / % possible all: 90.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4AW9 AND 4N6L

4aw9

4n6l


Resolution: 1.87→44.5 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.896 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.165 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21937 1778 5 %RANDOM
Rwork0.21364 ---
all0.21393 35804 --
obs0.2136 34006 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.562 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.72 Å2
2---0.79 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.87→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 72 244 3342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193173
X-RAY DIFFRACTIONr_bond_other_d0.0010.022911
X-RAY DIFFRACTIONr_angle_refined_deg0.9831.9624314
X-RAY DIFFRACTIONr_angle_other_deg0.6743.0016680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08424.671152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07315519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2921513
X-RAY DIFFRACTIONr_chiral_restr0.0550.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02741
X-RAY DIFFRACTIONr_mcbond_it0.4472.1211513
X-RAY DIFFRACTIONr_mcbond_other0.4472.121512
X-RAY DIFFRACTIONr_mcangle_it0.8373.1781886
X-RAY DIFFRACTIONr_mcangle_other0.8363.1791887
X-RAY DIFFRACTIONr_scbond_it0.342.141660
X-RAY DIFFRACTIONr_scbond_other0.3392.1391658
X-RAY DIFFRACTIONr_scangle_other0.6213.1942417
X-RAY DIFFRACTIONr_long_range_B_refined2.98317.0263725
X-RAY DIFFRACTIONr_long_range_B_other2.68516.7043628
LS refinement shellResolution: 1.87→1.916 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 127 -
Rwork0.282 2115 -
obs--83.47 %

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