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- PDB-10jz: Structure of the human CHI3L1-LZ6 complex -

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Basic information

Entry
Database: PDB / ID: 10jz
TitleStructure of the human CHI3L1-LZ6 complex
ComponentsChitinase-3-like protein 1
KeywordsHYDROLASE / CHI3L1 / Glycosyl hydrolase 18 / Glioblastoma / CHI-LZ6 complex / SPR screening
Function / homology
Function and homology information


transforming growth factor beta1 production / response to interleukin-6 / cartilage development / chitin catabolic process / chitin binding / extracellular matrix structural constituent / lung development / ERK1 and ERK2 cascade / response to tumor necrosis factor / response to mechanical stimulus ...transforming growth factor beta1 production / response to interleukin-6 / cartilage development / chitin catabolic process / chitin binding / extracellular matrix structural constituent / lung development / ERK1 and ERK2 cascade / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of interleukin-8 production / cellular response to tumor necrosis factor / specific granule lumen / positive regulation of angiogenesis / carbohydrate binding / extracellular matrix / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / apoptotic process / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / : / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
: / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Chitinase-3-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsUpadhyay, S. / Zhang, L. / Teplova, M. / Gabr, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS136524 United States
CitationJournal: To Be Published
Title: Structure of the human CHI3L1 i-LZ6 complex.
Authors: Upadhyay, S. / Zhang, L. / Teplova, M. / Gabr, M.
History
DepositionJan 22, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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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)183,18718
Polymers179,3594
Non-polymers3,82814
Water2,684149
1
A: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8365
Polymers44,8401
Non-polymers9964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8365
Polymers44,8401
Non-polymers9964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7584
Polymers44,8401
Non-polymers9183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7584
Polymers44,8401
Non-polymers9183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.302, 122.352, 136.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Chitinase-3-like protein 1 / 39 kDa synovial protein / Cartilage glycoprotein 39 / CGP-39 / GP-39 / hCGP-39 / YKL-40


Mass: 44839.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHI3L1 / Production host: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 159 molecules

#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-A1DAW / N-(1-ethyl-6-oxo-1,6-dihydropyrimidin-5-yl)-4-(2-methyl-4-oxoquinazolin-3(4H)-yl)benzamide


Mass: 401.418 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H19N5O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium chloride dihydrate, 0.1 M MES monohydrate, pH 6.0, 20% (w/v) PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 22, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.61→33.83 Å / Num. obs: 52412 / % possible obs: 93.8 % / Redundancy: 4.7 % / CC1/2: 0.966 / Rmerge(I) obs: 0.343 / Rpim(I) all: 0.161 / Rrim(I) all: 0.381 / Χ2: 0.97 / Net I/σ(I): 3.7 / Num. measured all: 245810
Reflection shellResolution: 2.61→2.75 Å / % possible obs: 84.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 1.911 / Num. measured all: 30345 / Num. unique obs: 6779 / CC1/2: 0.4 / Rpim(I) all: 0.911 / Rrim(I) all: 2.128 / Χ2: 0.95 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→33.83 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1998 4.37 %
Rwork0.1944 --
obs0.1964 45761 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11391 0 264 149 11804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911967
X-RAY DIFFRACTIONf_angle_d1.1316214
X-RAY DIFFRACTIONf_dihedral_angle_d16.3714380
X-RAY DIFFRACTIONf_chiral_restr0.0621718
X-RAY DIFFRACTIONf_plane_restr0.0122065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.30971490.26213264X-RAY DIFFRACTION100
2.82-2.890.27271470.25323211X-RAY DIFFRACTION100
2.89-2.980.32491480.25383246X-RAY DIFFRACTION100
2.98-3.080.3011480.24343216X-RAY DIFFRACTION100
3.08-3.190.3021470.23923226X-RAY DIFFRACTION99
3.19-3.310.29781470.22353262X-RAY DIFFRACTION99
3.31-3.460.26051150.22012512X-RAY DIFFRACTION78
3.46-3.640.28021410.20723080X-RAY DIFFRACTION97
3.66-3.870.21821270.17332797X-RAY DIFFRACTION92
3.88-4.170.19581320.1632887X-RAY DIFFRACTION88
4.17-4.590.19521460.14943189X-RAY DIFFRACTION97
4.59-5.250.18471490.1533255X-RAY DIFFRACTION98
5.26-6.610.21471490.18253282X-RAY DIFFRACTION98
6.61-33.830.1991530.18023336X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -40.8521 Å / Origin y: -0.7447 Å / Origin z: 34.0902 Å
111213212223313233
T0.1615 Å20.0023 Å20.011 Å2-0.1993 Å2-0.0026 Å2--0.1937 Å2
L0.3847 °20.0349 °2-0.0286 °2-0.57 °20.0036 °2--0.4366 °2
S0.0333 Å °0.024 Å °0.0716 Å °0.022 Å °-0.0122 Å °0.0624 Å °0.0032 Å °-0.1202 Å °-0.0287 Å °
Refinement TLS groupSelection details: all

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