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- PDB-8df1: Chi3l1 bound by antibody C59 -

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Basic information

Entry
Database: PDB / ID: 8df1
TitleChi3l1 bound by antibody C59
Components
  • C59 Fab Heavy chain
  • C59 Fab Light chain
  • Chitinase-3-like protein 1
KeywordsIMMUNE SYSTEM / Chi3l1 / Fab / immunotherapeutic
Function / homology
Function and homology information


response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / positive regulation of peptidyl-threonine phosphorylation / extracellular matrix structural constituent / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / positive regulation of peptidyl-threonine phosphorylation / extracellular matrix structural constituent / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix / lung development / response to interleukin-1 / positive regulation of interleukin-8 production / specific granule lumen / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / carbohydrate metabolic process / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / inflammatory response / apoptotic process / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / 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)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWrapp, D. / McLellan, J.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Antib Ther / Year: 2023
Title: A novel humanized Chi3l1 blocking antibody attenuates acetaminophen-induced liver injury in mice.
Authors: Li, L. / Wen, Y. / Wrapp, D. / Jeong, J. / Zhao, P. / Xiong, W. / Atkins, C.L. / Shan, Z. / Hui, D. / McLellan, J.S. / Zhang, N. / Ju, C. / An, Z.
History
DepositionJun 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _pdbx_entry_details.has_protein_modification

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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
E: Chitinase-3-like protein 1
F: Chitinase-3-like protein 1
M: C59 Fab Heavy chain
N: C59 Fab Light chain
H: C59 Fab Heavy chain
L: C59 Fab Light chain
O: C59 Fab Heavy chain
P: C59 Fab Light chain
Q: C59 Fab Heavy chain
R: C59 Fab Light chain
S: C59 Fab Heavy chain
T: C59 Fab Light chain
U: C59 Fab Heavy chain
V: C59 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)524,62124
Polymers520,45318
Non-polymers4,1686
Water00
1
A: Chitinase-3-like protein 1
H: C59 Fab Heavy chain
L: C59 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4914
Polymers86,7423
Non-polymers7491
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase-3-like protein 1
M: C59 Fab Heavy chain
N: C59 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3294
Polymers86,7423
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chitinase-3-like protein 1
O: C59 Fab Heavy chain
P: C59 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6534
Polymers86,7423
Non-polymers9111
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chitinase-3-like protein 1
Q: C59 Fab Heavy chain
R: C59 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3294
Polymers86,7423
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Chitinase-3-like protein 1
S: C59 Fab Heavy chain
T: C59 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4914
Polymers86,7423
Non-polymers7491
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Chitinase-3-like protein 1
U: C59 Fab Heavy chain
V: C59 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3294
Polymers86,7423
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.100, 172.920, 404.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 40536.758 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHI3L1 / Production host: Homo sapiens (human) / References: UniProt: P36222

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Antibody , 2 types, 12 molecules MHOQSUNLPRTV

#2: Antibody
C59 Fab Heavy chain


Mass: 23486.350 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Antibody
C59 Fab Light chain


Mass: 22719.049 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)

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Sugars , 3 types, 6 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Details

Has ligand of interestN
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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 10% PEG 4000, 2% MPD

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.3→87.29 Å / Num. obs: 108604 / % possible obs: 99.86 % / Redundancy: 11.8 % / Biso Wilson estimate: 56.88 Å2 / Rmerge(I) obs: 0.796 / Net I/σ(I): 8.97
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 1.87 / Num. unique obs: 10701 / CC1/2: 0.421 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P8V, 6PEH, 4HBC

4p8v

6peh

4hbc


Resolution: 3.3→87.29 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2432 --
Rwork0.2057 --
obs-108487 99.86 %
Displacement parametersBiso max: 241.48 Å2 / Biso mean: 71.1652 Å2 / Biso min: 21.74 Å2
Refinement stepCycle: LAST / Resolution: 3.3→87.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36612 0 278 0 36890

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