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- PDB-9dft: G1 domain of human aggrecan -

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Basic information

Entry
Database: PDB / ID: 9dft
TitleG1 domain of human aggrecan
ComponentsAggrecan core protein
KeywordsSUGAR BINDING PROTEIN / Extracellular matrix / hyaluronan / chondroitin sulfate proteoglycan
Function / homology
Function and homology information


Defective CHST6 causes MCDC1 / Defective ST3GAL3 causes MCT12 and EIEE15 / perineuronal net / Keratan sulfate degradation / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Keratan sulfate biosynthesis / hyaluronic acid binding / extracellular matrix structural constituent / ECM proteoglycans / Degradation of the extracellular matrix ...Defective CHST6 causes MCDC1 / Defective ST3GAL3 causes MCT12 and EIEE15 / perineuronal net / Keratan sulfate degradation / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Keratan sulfate biosynthesis / hyaluronic acid binding / extracellular matrix structural constituent / ECM proteoglycans / Degradation of the extracellular matrix / lysosomal lumen / central nervous system development / skeletal system development / Golgi lumen / carbohydrate binding / : / cell adhesion / synapse / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Aggrecan/versican, C-type lectin-like domain / : / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) ...Aggrecan/versican, C-type lectin-like domain / : / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Aggrecan core protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBouyains, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143757 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Aggrecan immobilizes to perineuronal nets through hyaluronan-dependent and hyaluronan-independent binding activities.
Authors: Otsuka, M.Y. / Essel, L.B. / Sinha, A. / Nickerson, G. / Mejia, S.M. / Edge, A. / Matthews, R.T. / Bouyain, S.
History
DepositionAug 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 11, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aggrecan core protein
B: Aggrecan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6199
Polymers74,3212
Non-polymers1,2987
Water00
1
A: Aggrecan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8244
Polymers37,1611
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aggrecan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7955
Polymers37,1611
Non-polymers6354
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.480, 121.480, 213.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Aggrecan core protein / Cartilage-specific proteoglycan core protein / CSPCP / Chondroitin sulfate proteoglycan core ...Cartilage-specific proteoglycan core protein / CSPCP / Chondroitin sulfate proteoglycan core protein 1 / Chondroitin sulfate proteoglycan 1


Mass: 37160.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACAN, AGC1, CSPG1, MSK16 / Production host: Homo sapiens (human) / References: UniProt: P16112
#2: 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.: 5 / Source method: obtained synthetically / 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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: 5.3 Å3/Da / Density % sol: 76.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1% (m/v) PEG 3,350, 100 mM Bis-Tris pH 5.5, 600 mM (NH4)2SO4

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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: Jul 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→85.91 Å / Num. obs: 20877 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 152.48 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.044 / Rrim(I) all: 0.133 / Net I/σ(I): 7.5
Reflection shellResolution: 3.5→3.83 Å / Rmerge(I) obs: 1.393 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4880 / CC1/2: 0.683 / Rpim(I) all: 0.664 / Rrim(I) all: 1.476 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→61.38 Å / SU ML: 0.4772 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 2084 10.01 %
Rwork0.1983 18740 -
obs0.203 20824 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 167.78 Å2
Refinement stepCycle: LAST / Resolution: 3.5→61.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 80 0 4758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194864
X-RAY DIFFRACTIONf_angle_d0.50676617
X-RAY DIFFRACTIONf_chiral_restr0.0447740
X-RAY DIFFRACTIONf_plane_restr0.0048855
X-RAY DIFFRACTIONf_dihedral_angle_d11.47251858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.580.42661370.33381232X-RAY DIFFRACTION99.85
3.58-3.670.32341350.29681219X-RAY DIFFRACTION99.93
3.67-3.770.30571340.25151210X-RAY DIFFRACTION100
3.77-3.880.27151380.2371230X-RAY DIFFRACTION99.93
3.88-4.010.24121350.22651220X-RAY DIFFRACTION100
4.01-4.150.25581360.18671230X-RAY DIFFRACTION100
4.15-4.320.21081400.15971256X-RAY DIFFRACTION100
4.32-4.510.18361360.14671218X-RAY DIFFRACTION99.85
4.51-4.750.18461370.13931232X-RAY DIFFRACTION99.93
4.75-5.050.18931390.15871260X-RAY DIFFRACTION100
5.05-5.440.19611380.15921238X-RAY DIFFRACTION100
5.44-5.980.25861390.1811262X-RAY DIFFRACTION99.93
5.98-6.850.28251440.20951277X-RAY DIFFRACTION100
6.85-8.620.27671430.20331293X-RAY DIFFRACTION100
8.63-61.380.24421530.22811363X-RAY DIFFRACTION98.44
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)
16.73439591593-0.341995465593.474424808354.819619031.488130703854.58870845763-0.1340596994730.4403432847940.8966228538480.192899590072-0.0416200763798-0.149062032029-0.460415407718-0.3868987972910.1730814378521.35889192460.0726357569818-0.02735441705191.405877610090.267353983351.52949111843-12.665469128439.9975901678-15.802163284
21.821793643080.4163402383610.8059303029263.397287808370.7118097953515.821352920950.0378434777584-0.83929537721-0.3368667869850.472034391925-0.319397180496-0.0316321166641.19008549453-0.3259212560390.311431231721.20934507527-0.01482300360930.03781679088091.575142591170.309514888661.39355092715-39.734243600227.4765782432-30.9371702968
32.8990493993-2.516191152480.04111717058032.481976469460.9137008775172.82911417036-0.103917089826-0.9307868751960.3263789998540.06092729057940.415878992081-0.0145784786477-0.128993649866-0.0511567051439-0.2950273107841.322910309450.02351451786520.1475982629051.51676678320.1412003498231.37403457967-41.113017518238.7377007995-38.8772984437
41.53121102673-0.142996033694-0.05996881209142.51355250406-1.538373769984.93727365211-0.0247743260658-0.154107059605-0.06204151246280.1987947881780.1226136719390.4564218363090.381347199861-0.735506696359-0.1596128696931.11617643515-0.0850832162063-0.02812928667521.333008354110.2201540003071.44965516788-1.9250154172912.53144250387.68729940592
54.840605637041.57609780351-1.108752275094.756455954370.4735956914255.52137244181-0.0397629064415-0.9553613927750.3388422924220.4218497810320.3216461526821.598752017732.32357277486-3.436822844730.2414919586411.88867354383-0.2531696108280.5891779568842.43219083790.8005647743932.23206412694-13.63616201123.6501296631327.4545392512
63.590070414920.2051638685871.530420219340.474914679305-1.375306217875.247725735520.615391177778-2.14128737672-0.3334388643750.2553316845860.09273004327870.5898586838610.407948603732-2.54872359529-0.6874184385941.64613697384-0.03523887066330.4897438258372.354073190640.6371556135252.00154796739-13.5147549437.1622948205131.3869741001
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 29 through 151 )AA29 - 1511 - 109
22chain 'A' and (resid 152 through 306 )AA152 - 306110 - 264
33chain 'A' and (resid 307 through 350 )AA307 - 350265 - 308
44chain 'B' and (resid 27 through 291 )BE27 - 2911 - 228
55chain 'B' and (resid 292 through 311 )BE292 - 311229 - 248
66chain 'B' and (resid 312 through 350 )BE312 - 350249 - 287

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