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- PDB-1hjx: Ligand-induced signalling and conformational change of the 39 kD ... -

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Basic information

Entry
Database: PDB / ID: 1hjx
TitleLigand-induced signalling and conformational change of the 39 kD glycoprotein from human articular chondrocytes
ComponentsCHITINASE-3 LIKE PROTEIN 1
KeywordsSUGAR BINDING PROTEIN / LECTIN / CHI-LECTIN / CHITINASE / ARTHRISTIS / CHONDROCYTES
Function / homology
Function and homology information


response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin catabolic process / cartilage development / extracellular matrix structural constituent / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix / response to interleukin-1 ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin catabolic process / cartilage development / extracellular matrix structural constituent / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / specific granule lumen / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / carbohydrate metabolic process / inflammatory response / apoptotic process / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily ...Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chitinase-3-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHouston, D.R. / Recklies, A.D. / Krupa, J.C. / Van Aalten, D.M.F.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure and Ligand-Induced Conformational Change of the 39-kDa Glycoprotein from Human Articular Chondrocytes
Authors: Houston, D.R. / Recklies, A.D. / Krupa, J.C. / Van Aalten, D.M.F.
History
DepositionFeb 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / 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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHITINASE-3 LIKE PROTEIN 1
B: CHITINASE-3 LIKE PROTEIN 1
C: CHITINASE-3 LIKE PROTEIN 1
D: CHITINASE-3 LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,08732
Polymers162,1474
Non-polymers3,94028
Water25,0951393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.562, 122.048, 136.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CHITINASE-3 LIKE PROTEIN 1 / CARTILAGE GLYCOPROTEIN-39 / GP-39 / 39 KDA SYNOVIAL PROTEIN / YKL-40


Mass: 40536.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: CHONDROCYTES / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P36222
#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.: 4
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1393 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMAY PLAY AN IMPORTANT ROLE IN THE CAPACITY OF CELLS TO RESPOND TO AND COPE WITH CHANGES IN THEIR ENVIRONMENT.
Sequence detailsPOLYMORPHISM AT RESIDE 311

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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 %
Crystal growpH: 4.6
Details: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE PH 4.6, 25% PEG 4000, 100 MM DTT

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976219
DetectorDetector: CCD / Date: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976219 Å / Relative weight: 1
ReflectionResolution: 1.85→15 Å / Num. obs: 153614 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.7 / % possible all: 98.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
FFFEARphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LG2

1lg2


Resolution: 1.85→14.98 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3069738.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 728 0.5 %RANDOM
Rwork0.197 ---
obs0.197 153536 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.3874 Å2 / ksol: 0.357941 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.26 Å20 Å20 Å2
2---1.25 Å20 Å2
3---8.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.85→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11380 0 248 1393 13021
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.452.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 131 0.5 %
Rwork0.28 24914 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GLYCEROL.PARAMGLYCEROL.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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