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- PDB-3k24: Crystal structure of mature apo-Cathepsin L C25A mutant in comple... -

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Basic information

Entry
Database: PDB / ID: 3k24
TitleCrystal structure of mature apo-Cathepsin L C25A mutant in complex with Gln-Leu-Ala peptide
Components
  • Cathepsin L1
  • H3 peptide
KeywordsHYDROLASE / co-crystal / substrate / protease / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / zymogen activation / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / antigen processing and presentation / Collagen degradation / protein autoprocessing / fibronectin binding / collagen catabolic process / serpin family protein binding / collagen binding / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / Degradation of the extracellular matrix / multivesicular body / endocytic vesicle lumen / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / : / adaptive immune response / histone binding / Attachment and Entry / lysosome / apical plasma membrane / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
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 ...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: 2.5 Å
AuthorsAdams-Cioaba, M.A. / Krupa, J.C. / Mort, J.S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2011
Title: Structural basis for the recognition and cleavage of histone H3 by cathepsin L.
Authors: Adams-Cioaba, M.A. / Krupa, J.C. / Xu, C. / Mort, J.S. / Min, J.
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin L1
B: Cathepsin L1
C: H3 peptide
D: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3156
Polymers48,9804
Non-polymers1,3352
Water57632
1
A: Cathepsin L1
D: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7113
Polymers24,4902
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-3.8 kcal/mol
Surface area9940 Å2
MethodPISA
2
B: Cathepsin L1
C: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6043
Polymers24,4902
Non-polymers1,1141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-3.4 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.697, 62.697, 205.868
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
DetailsThe biological unit is a monomeric complex of the protein with peptide. Word "dimeric" in remark 350 is incorrect as it is only chain count.

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Components

#1: Protein Cathepsin L1 / Major excreted protein / MEP / Cathepsin L1 heavy chain and Cathepsin L1 light chain


Mass: 24159.639 Da / Num. of mol.: 2 / Fragment: mC25A: UNP residues 114-333 / Mutation: C138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL1, CTSL / Production host: Pichia pastoris (fungus) / References: UniProt: P07711, cathepsin L
#2: Protein/peptide H3 peptide


Mass: 330.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-6)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-6)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-6DManpb1-6[DManpa1-2]DManpa1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-2-3-3-4-2/a4-b1_b4-c1_c2-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{[(6+1)][a-D-GlcpNAc]{}}}}}}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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 10% Isopropanol, 0.1 M Sodium acetate trihydrate pH 4.0, 22% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2009 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 17063 / Num. obs: 15954 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rsym value: 0.074 / Net I/σ(I): 31.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 6 / Num. unique all: 983 / Rsym value: 0.198 / % possible all: 59.1

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Processing

Software
NameVersionClassification
Blu-IceGUI (SSRL) modified by GM/CATdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IV2

3iv2


Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 22.192 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.996 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27002 823 5.1 %RANDOM
Rwork0.20926 ---
obs0.2124 15283 94.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.809 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å20 Å2
2--0.69 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 89 32 3557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0223620
X-RAY DIFFRACTIONr_angle_refined_deg0.5451.974910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4815442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24425.233172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.79915556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2561512
X-RAY DIFFRACTIONr_chiral_restr0.0460.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212802
X-RAY DIFFRACTIONr_mcbond_it1.1081.52196
X-RAY DIFFRACTIONr_mcangle_it1.94223488
X-RAY DIFFRACTIONr_scbond_it3.28431424
X-RAY DIFFRACTIONr_scangle_it5.1244.51422
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1696 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.250.5
medium thermal1.382
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 29 -
Rwork0.232 706 -
obs--60.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.63290.4266-0.15071.7951-0.16651.82790.0395-0.15250.02080.1546-0.0293-0.08860.2494-0.1406-0.01020.13830.0020.00670.164-0.0190.02515.4940.4009-18.8503
21.10161.34320.40983.62010.80023.14880.2505-0.0244-0.20420.547-0.2681-0.54150.16670.58460.01760.11620.0181-0.09410.31430.10690.22713.9897-27.1625-9.2215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 220
2X-RAY DIFFRACTION1B221 - 226
3X-RAY DIFFRACTION1B227 - 246
4X-RAY DIFFRACTION2A1 - 220
5X-RAY DIFFRACTION2A221
6X-RAY DIFFRACTION2A222 - 233

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