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- PDB-1nwt: Crystal structure of human cartilage gp39 (HC-gp39) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 1nwt
TitleCrystal structure of human cartilage gp39 (HC-gp39) in complex with chitopentaose
ComponentsChitinase-3 like protein 1
KeywordsSIGNALING PROTEIN / chitinase-like protein / rheumatoid arthritis / chitin / N-acetylglucosamine
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFusetti, F. / Pijning, T. / Kalk, K.H. / Bos, E. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure and carbohydrate-binding properties of the human cartilage glycoprotein-39
Authors: Fusetti, F. / Pijning, T. / Kalk, K.H. / Bos, E. / Dijkstra, B.W.
History
DepositionFeb 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_database_remark / Item: _diffrn_source.type / _pdbx_database_remark.text
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_ref_seq_dif / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _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_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_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEET PRESENTED AS A1 ON SHEET RECORDS BELOW IS ACTUALLY AN ... SHEET DETERMINATION METHOD: DSSP THE SHEET PRESENTED AS A1 ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED ALPHA/BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS B1 ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED ALPHA/BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS C1 ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED ALPHA/BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS D1 ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED ALPHA/BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEETS A3A AND A3B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS SPLIT INTO TWO DISTINCT AMINO ACID RUNS. THE BULGE OF 11 AMINO ACIDS (RESIDUES 282-292) INCLUDES A HYDROGEN-BONDED TURN (RESIDUES 286-292). SHEETS B3A AND B3B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS SPLIT INTO TWO DISTINCT AMINO ACID RUNS. THE BULGE OF 11 AMINO ACIDS (RESIDUES 282-292) INCLUDES A HYDROGEN-BONDED TURN (RESIDUES 286-292). SHEETS C3A AND C3B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS SPLIT INTO TWO DISTINCT AMINO ACID RUNS. THE BULGE OF 11 AMINO ACIDS (RESIDUES 282-292) INCLUDES A HYDROGEN-BONDED TURN (RESIDUES 286-292). SHEETS D3A AND D3B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS SPLIT INTO TWO DISTINCT AMINO ACID RUNS. THE BULGE OF 11 AMINO ACIDS (RESIDUES 282-292) INCLUDES A HYDROGEN-BONDED TURN (RESIDUES 286-292).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)168,59012
Polymers162,1474
Non-polymers6,4438
Water8,467470
1
A: Chitinase-3 like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1983
Polymers40,5371
Non-polymers1,6622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase-3 like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9953
Polymers40,5371
Non-polymers1,4582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chitinase-3 like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1983
Polymers40,5371
Non-polymers1,6622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chitinase-3 like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1983
Polymers40,5371
Non-polymers1,6622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.320, 128.320, 108.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: synovial cells, articular chondrocytes / Cell (production host): mammalian cho cells / Production host: Cricetulus griseus (Chinese hamster) / 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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAca1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-1-1-1-2-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1033.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAca1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 50.23 %
Crystal growpH: 5.1 / Details: pH 5.1
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14 mg/mlprotein1drop
21 M1dropNaCl
310 mMBES1droppH7.2
410 %PEG80001reservoir
50.5 M1reservoirNaCl
60.1 Msodium citrate1reservoirpH5.1

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→29.92 Å / Num. obs: 59975 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 45.5 Å2 / Rsym value: 0.114 / Net I/σ(I): 10.1
Reflection shellHighest resolution: 2.5 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.626 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. measured all: 227637 / Rmerge(I) obs: 0.114
Reflection shell
*PLUS
% possible obs: 96.1 % / Rmerge(I) obs: 0.626

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2447799.71 / Data cutoff high rms absF: 2447799.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE IMPOSED ON THE FOLLOWING RESIDUE GROUPS IN ALL FOUR MOLECULES: GROUP 1: RESIDUES 22 TO 208, GROUP 2: RESIDUES 214 TO 226, GROUP 3: RESIDUES 235 ...Details: NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE IMPOSED ON THE FOLLOWING RESIDUE GROUPS IN ALL FOUR MOLECULES: GROUP 1: RESIDUES 22 TO 208, GROUP 2: RESIDUES 214 TO 226, GROUP 3: RESIDUES 235 TO 242, GROUP 4: RESIDUES 249 to 383
RfactorNum. reflection% reflectionSelection details
Rfree0.253 8129 13.6 %RANDOM
Rwork0.218 ---
obs0.218 59975 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.53 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.78 Å20 Å20 Å2
2--5.78 Å20 Å2
3----11.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11361 0 438 470 12269
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.71.5
X-RAY DIFFRACTIONc_mcangle_it4.032
X-RAY DIFFRACTIONc_scbond_it4.222
X-RAY DIFFRACTIONc_scangle_it5.712.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 833 8.6 %
Rwork0.335 8896 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
X-RAY DIFFRACTION5
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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