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- PDB-8v58: Complex of murine cathepsin K with bound heparan sulfate 12mer -

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Basic information

Entry
Database: PDB / ID: 8v58
TitleComplex of murine cathepsin K with bound heparan sulfate 12mer
ComponentsCathepsin K
KeywordsHYDROLASE / complex / heparan sulfate / protease / collagenase
Function / homology
Function and homology information


RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Activation of Matrix Metalloproteinases / Collagen degradation / Trafficking and processing of endosomal TLR / cathepsin K / mononuclear cell differentiation / Degradation of the extracellular matrix / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation ...RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Activation of Matrix Metalloproteinases / Collagen degradation / Trafficking and processing of endosomal TLR / cathepsin K / mononuclear cell differentiation / Degradation of the extracellular matrix / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / MHC class II antigen presentation / thyroid hormone generation / proteoglycan binding / fibronectin binding / collagen catabolic process / bone resorption / cellular response to transforming growth factor beta stimulus / collagen binding / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / response to insulin / : / cellular response to tumor necrosis factor / response to ethanol / lysosome / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / extracellular space / nucleoplasm
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / 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 ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPedersen, L.C. / Xu, D. / Krahn, J.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC-ES102645 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE031273 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR070179 United States
CitationJournal: Matrix Biol. / Year: 2024
Title: Heparan sulfate selectively inhibits the collagenase activity of cathepsin K.
Authors: Zhang, X. / Luo, Y. / Hao, H. / Krahn, J.M. / Su, G. / Dutcher, R. / Xu, Y. / Liu, J. / Pedersen, L.C. / Xu, D.
History
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin K
B: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6396
Polymers47,3252
Non-polymers4,3144
Water181
1


  • Idetical with deposited unit
  • defined by author
  • dimeric, unknown dimer interface
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.892, 111.892, 116.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cathepsin K


Mass: 23662.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctsk / Cell line (production host): HEK293-freestyle / Production host: Homo sapiens (human) / Strain (production host): HEK293 / References: UniProt: P55097

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Sugars , 3 types, 3 molecules

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


Type: oligosaccharide / Mass: 1381.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DManpa1-4DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-3-3-4-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e4-f1_f4-g1WURCSPDB2Glycan 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]{[(4+1)][a-D-Manp]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid


Type: oligosaccharide / Mass: 2649.180 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,8,7/[a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2-1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][L-1,6-deoxy-Idop2SO3]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-6-deoxy-Idop2SO3]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-6-deoxy-Idop2SO3]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-6-deoxy-Idop2SO3]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{}}}}}}}}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 , 2 types, 2 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
Nonpolymer detailsThe conformation of the 12mer oligosaccharide represents the best fit of the heparan sulfate ...The conformation of the 12mer oligosaccharide represents the best fit of the heparan sulfate oligosaccharide to the electron density. Difference density suggests alternate conformations likely also exist.

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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: 3.86 Å3/Da / Density % sol: 68.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M sodium acetate, 0.2M lithium sulfate, 31.5% PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13901 / % possible obs: 98.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 92.46 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.036 / Rrim(I) all: 0.099 / Rsym value: 0.092 / Net I/σ(I): 5.4
Reflection shellResolution: 3.1→3.15 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 675 / CC1/2: 0.875 / Rpim(I) all: 0.361 / Rrim(I) all: 1.03 / Rsym value: 0.963

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.87 Å / SU ML: 0.4078 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.4323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2926 686 5.03 %
Rwork0.2359 12961 -
obs0.2386 13647 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.75 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 252 1 3422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873487
X-RAY DIFFRACTIONf_angle_d1.29794757
X-RAY DIFFRACTIONf_chiral_restr0.0758560
X-RAY DIFFRACTIONf_plane_restr0.0082589
X-RAY DIFFRACTIONf_dihedral_angle_d17.61911276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.340.33431300.30292499X-RAY DIFFRACTION97.15
3.34-3.670.31551360.2482557X-RAY DIFFRACTION98.43
3.67-4.20.29091380.22812586X-RAY DIFFRACTION98.95
4.2-5.270.24831380.21962630X-RAY DIFFRACTION99.21
5.27-19.870.30531440.23312689X-RAY DIFFRACTION96.46
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)
11.814636641480.812180234840.6253112346322.213394084010.7355390728834.388363567040.1257249210840.190666029261-0.0689733093069-0.1488156566060.208129576449-0.280909477346-0.4561048310160.170379072208-4.89812465961E-91.003047460170.1185056816060.02519616910961.1588545494-0.1813782496121.0303114358623.119-11.005-0.281
20.356210824176-0.3290504463631.00976908274.122923454751.273975936383.292064847090.3764054288170.00895248060833-0.597059855929-0.0900475021605-0.197117328037-0.378943773020.946256844055-0.0229226142225-0.1465902801811.549791882620.144504856401-0.2391687007011.17674848261-0.3639465835951.5345862257723.136-45.669-13.212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:215 )A1 - 215
2X-RAY DIFFRACTION2( CHAIN B AND ( RESID 1:215 OR RESID 401:401 ) )B1 - 215
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 1:215 OR RESID 401:401 ) )B401

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