[English] 日本語
Yorodumi
- PDB-9dff: G1 domain of human aggrecan bound to hyaluronan -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dff
TitleG1 domain of human aggrecan bound to hyaluronan
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: 2.59 Å
AuthorsBouyain, 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 29, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,44110
Polymers74,3212
Non-polymers5,1208
Water3,117173
1
A: Aggrecan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7215
Polymers37,1611
Non-polymers2,5604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aggrecan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7215
Polymers37,1611
Non-polymers2,5604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.067, 64.943, 112.206
Angle α, β, γ (deg.)90.000, 109.327, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
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: Polysaccharide 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1896.583 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5][a21eEA-1a_1-5]/1-2-1-2-1-2-1-2-1-3/a3-b1_b4-c1_c3-d1_d4-e1_e3-f1_f4-g1_g3-h1_h4-i1_i3-j1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-4-deoxy-IdopA]{}}}}}}}}}}LINUCSPDB-CARE
#3: 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.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 10,000, 50 mM Bis-Tris propane 9.0, 200 mM NH4OAc

-
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: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 29486 / % possible obs: 96.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 38.31 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.104 / Rrim(I) all: 0.194 / Net I/σ(I): 6.08
Reflection shellResolution: 2.58→2.67 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 2940 / CC1/2: 0.731 / Rpim(I) all: 0.361 / Rrim(I) all: 0.655

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→41.03 Å / SU ML: 0.3768 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 26.8926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2376 1884 6.78 %
Rwork0.1937 25921 -
obs0.1968 27805 89.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.73 Å2
Refinement stepCycle: LAST / Resolution: 2.59→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 344 173 5297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00485269
X-RAY DIFFRACTIONf_angle_d0.7267178
X-RAY DIFFRACTIONf_chiral_restr0.0503856
X-RAY DIFFRACTIONf_plane_restr0.0077906
X-RAY DIFFRACTIONf_dihedral_angle_d12.63772332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.660.3245960.26071316X-RAY DIFFRACTION60.29
2.66-2.740.31291400.26411888X-RAY DIFFRACTION84.78
2.74-2.830.36181370.26051955X-RAY DIFFRACTION87.2
2.83-2.930.3191380.26161999X-RAY DIFFRACTION90.13
2.93-3.040.31451500.24122025X-RAY DIFFRACTION91.04
3.04-3.180.30541490.22722049X-RAY DIFFRACTION92.24
3.18-3.350.28321490.2172062X-RAY DIFFRACTION92.63
3.35-3.560.23891600.20792110X-RAY DIFFRACTION95.06
3.56-3.830.22231590.18182160X-RAY DIFFRACTION95.87
3.83-4.220.20261550.15832088X-RAY DIFFRACTION93.65
4.22-4.830.17521400.15052018X-RAY DIFFRACTION89.58
4.83-6.080.19351510.15342114X-RAY DIFFRACTION92.9
6.08-41.030.19591600.18332137X-RAY DIFFRACTION92.1
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)
11.709477485530.48638559421-0.02624599638581.544799494221.077319783290.8623862533640.0341894396710.02112056968490.421424679641-0.2423744049740.05413079935471.14657602357-0.117488652729-0.0260560000297-0.0980963736620.328559418154-0.00332216124498-0.0800783171820.3740961961660.01636014645330.72712145598314.21514.425-2.337
21.232927209510.438727088603-0.3186222295362.41117915906-0.4151272002261.00645775965-0.0386732125611-0.08999397276210.1341171726010.00845706747123-0.02517223431840.1645463248330.1036639117880.01229725544160.06220902112670.1941054023580.0140934754274-0.03862907123650.2770172157-0.01408428012760.19563437541924.732-12.3814.313
31.26169931791-0.8790245048710.5779844755342.93494140440.6023300707391.886340591680.2225552403120.109662558109-0.33334555018-0.0856827080512-5.07182365205E-51.232469431860.501975702690.0381668148093-0.1981609565420.5797340448090.0326328244507-0.03400543375530.3734862781870.01020170547610.669798821749-1.289-68.10741.442
41.01068888943-0.1826037749650.1387875757821.78262909507-0.8667984721670.9664438542310.103720730336-0.0537937019942-0.06986073168380.206957096888-0.03584869471570.169206356536-0.09417350780270.0221421433144-0.05541023670870.39208317779-0.01831317185990.06883184301380.306353056311-0.01047359897610.24560495733211.552-40.63642.519
53.227952416370.512528068075-1.044163676050.9908498274850.1955975742421.046594658460.257320888549-0.2273160571190.007436566188760.070676490598-0.3374075360890.0118950905861-0.0948629670897-0.08499533188250.05391557273990.3679692121470.0395509386674-0.05949673935840.4635903269060.0580604046290.23476285285436.123-13.05212.808
61.306752396-0.02127331247760.3969090266541.17843821717-0.687437701194.208954445590.1122038065230.17936883817-0.03210685560330.224028345372-0.02570037844410.2133428085720.004850267549720.362044663861-0.1009218498870.414214714246-0.04079633961080.06832782473170.4110926058980.02810281037540.33999073605325.692-40.56542.683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 30:128 OR RESID 401:401 ) )A30 - 128
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 30:128 OR RESID 401:401 ) )A401
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 129:350 OR RESID 402:402 OR RESID 403:403 ) )A129 - 350
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 129:350 OR RESID 402:402 OR RESID 403:403 ) )A402
5X-RAY DIFFRACTION2( CHAIN A AND ( RESID 129:350 OR RESID 402:402 OR RESID 403:403 ) )A403
6X-RAY DIFFRACTION3( CHAIN B AND ( RESID 31:128 OR RESID 401:401 ) )B31 - 128
7X-RAY DIFFRACTION3( CHAIN B AND ( RESID 31:128 OR RESID 401:401 ) )B401
8X-RAY DIFFRACTION4( CHAIN B AND ( RESID 129:350 OR RESID 402:402 OR RESID 403:403 ) )B129 - 350
9X-RAY DIFFRACTION4( CHAIN B AND ( RESID 129:350 OR RESID 402:402 OR RESID 403:403 ) )B402
10X-RAY DIFFRACTION4( CHAIN B AND ( RESID 129:350 OR RESID 402:402 OR RESID 403:403 ) )B403
11X-RAY DIFFRACTION5( CHAIN C AND RESID 1:10 )C1 - 10
12X-RAY DIFFRACTION6( CHAIN D AND RESID 1:10 )D1 - 10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more