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- PDB-4fgu: Crystal structure of prolegumain -

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Basic information

Entry
Database: PDB / ID: 4fgu
TitleCrystal structure of prolegumain
ComponentsLegumain
KeywordsHYDROLASE / CYSTEINE PROTEASE / AEP / ASPARAGINYL ENDOPEPTIDASE / SUBSTRATE SPECIFICITY / MHCII / ANTIGEN PROCESSING / PROENZYME / CANCER / LYSOSOMAL
Function / homology
Function and homology information


negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / vitamin D metabolic process / receptor catabolic process / self proteolysis / activation of cysteine-type endopeptidase activity / endolysosome lumen ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / vitamin D metabolic process / receptor catabolic process / self proteolysis / activation of cysteine-type endopeptidase activity / endolysosome lumen / response to acidic pH / dendritic spine organization / positive regulation of monocyte chemotaxis / 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 / protein maturation / endopeptidase activator activity / MHC class II antigen presentation / cellular response to calcium ion / lysosomal lumen / positive regulation of mitotic cell cycle / proteolysis involved in protein catabolic process / positive regulation of long-term synaptic potentiation / tau protein binding / memory / antigen processing and presentation of exogenous peptide antigen via MHC class II / cellular response to amyloid-beta / late endosome / apical part of cell / peptidase activity / negative regulation of neuron apoptotic process / lysosome / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Topoisomerase I; Chain A, domain 4 - #130 / Asparaginyl endopeptidase / Legumain prodomain superfamily / : / Legumain, prodomain / Peptidase C13, legumain / Peptidase C13 family / Topoisomerase I; Chain A, domain 4 / Rossmann fold - #1460 / Rossmann fold ...Topoisomerase I; Chain A, domain 4 - #130 / Asparaginyl endopeptidase / Legumain prodomain superfamily / : / Legumain, prodomain / Peptidase C13, legumain / Peptidase C13 family / Topoisomerase I; Chain A, domain 4 / Rossmann fold - #1460 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsDall, E. / Brandstetter, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Mechanistic and structural studies on legumain explain its zymogenicity, distinct activation pathways, and regulation.
Authors: Dall, E. / Brandstetter, H.
History
DepositionJun 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Legumain
B: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7026
Polymers98,4112
Non-polymers1,2914
Water1,00956
1
A: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8513
Polymers49,2051
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8513
Polymers49,2051
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Legumain
hetero molecules

B: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7026
Polymers98,4112
Non-polymers1,2914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area3480 Å2
ΔGint8 kcal/mol
Surface area33180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.100, 185.100, 173.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 49205.469 Da / Num. of mol.: 2 / Mutation: N272Q
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: 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.: 2
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 35 % 2-ethoxyethanol, 0.1 M cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 10, 2012
RadiationMonochromator: DOUBLE CRYSTAL (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→58.8 Å / Num. obs: 10515 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.9→4.11 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
PHASERphasing
REFMAC5.6.0117refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→49.63 Å / Cor.coef. Fo:Fc: 0.775 / Cor.coef. Fo:Fc free: 0.722 / SU B: 55.155 / SU ML: 0.76 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.975 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29963 503 4.8 %RANDOM
Rwork0.28582 ---
all0.2867 10515 --
obs0.28648 9976 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.383 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 3.9→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6548 0 84 56 6688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026820
X-RAY DIFFRACTIONr_bond_other_d0.0080.0228
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9589276
X-RAY DIFFRACTIONr_angle_other_deg1.809350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5695809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00524.012324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.034151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.8991534
X-RAY DIFFRACTIONr_chiral_restr0.070.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215202
X-RAY DIFFRACTIONr_gen_planes_other00.022
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 42 -
Rwork0.405 644 -
obs--97.3 %

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