[English] 日本語
Yorodumi
- EMDB-70100: Cryo-EM structure of the CHSY3-CHPF1 chondroitin synthase heterodimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70100
TitleCryo-EM structure of the CHSY3-CHPF1 chondroitin synthase heterodimer
Map data
Sample
  • Complex: CHSY3-CHPF1 heterocomplex
    • Protein or peptide: Chondroitin sulfate synthase 3
    • Protein or peptide: Chondroitin sulfate synthase 2
  • Ligand: MANGANESE (II) ION
  • Ligand: URIDINE-5'-DIPHOSPHATE
KeywordsChondroitin sulfate / Chondroitin sulfate synthase / SUGAR BINDING PROTEIN / TRANSFERASE
Function / homology
Function and homology information


glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase / N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase / glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity / N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity / CS-GAG biosynthesis / chondroitin sulfate proteoglycan biosynthetic process / Golgi cisterna membrane / mitochondrial matrix / Golgi membrane / metal ion binding / cytosol
Similarity search - Function
Chondroitin N-acetylgalactosaminyltransferase / : / Chondroitin N-acetylgalactosaminyltransferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Chondroitin sulfate synthase 3 / Chondroitin sulfate synthase 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Human adenovirus sp.
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsTehari D / Cortiella N / Perez C / Moremen K
Funding support United States, Switzerland, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM154846 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130915 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103390 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM158187 United States
Swiss National Science Foundation310030_207974 Switzerland
CitationJournal: To Be Published
Title: Structural basis of chondroitin sulfate backbone polymer synthesis
Authors: Tehari D / Cortiella N / Perez C / Moremen KW
History
DepositionApr 8, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70100.png

Downloads & links

-
Map

FileDownload / File: emd_70100.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.992 Å		1.08 Å/pix.
x 256 pix.
= 276.992 Å		1.08 Å/pix.
x 256 pix.
= 276.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.082 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.161
Minimum - Maximum-1.5234616 - 2.1873655
Average (Standard dev.)0.00016932923 (±0.045219447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.992 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_70100_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_70100_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_70100_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CHSY3-CHPF1 heterocomplex

EntireName: CHSY3-CHPF1 heterocomplex
Components
  • Complex: CHSY3-CHPF1 heterocomplex
    • Protein or peptide: Chondroitin sulfate synthase 3
    • Protein or peptide: Chondroitin sulfate synthase 2
  • Ligand: MANGANESE (II) ION
  • Ligand: URIDINE-5'-DIPHOSPHATE

-
Supramolecule #1: CHSY3-CHPF1 heterocomplex

SupramoleculeName: CHSY3-CHPF1 heterocomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Chondroitin sulfate synthase 3

MacromoleculeName: Chondroitin sulfate synthase 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase
Source (natural)Organism: Human adenovirus sp.
Molecular weightTheoretical: 97.018109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AELSERKRRG SSLCSYYGRS AAGPRAGAQQ PLPQPQSRPR QEQSPPPARQ DLQGPPLPEA APGITSFRSS PWQQPPPLQQ RRRGREPEG ATGLPGAPAA EGEPEEEDGG AAGQRRDGRP GSSHNGSGDG GAAAPSARPR DFLYVGVMTA QKYLGSRALA A QRTWARFI ...String:
AELSERKRRG SSLCSYYGRS AAGPRAGAQQ PLPQPQSRPR QEQSPPPARQ DLQGPPLPEA APGITSFRSS PWQQPPPLQQ RRRGREPEG ATGLPGAPAA EGEPEEEDGG AAGQRRDGRP GSSHNGSGDG GAAAPSARPR DFLYVGVMTA QKYLGSRALA A QRTWARFI PGRVEFFSSQ QPPNAGQPPP PLPVIALPGV DDSYPPQKKS FMMIKYMHDH YLDKYEWFMR ADDDVYIKGD KL EEFLRSL NSSKPLYLGQ TGLGNIEELG KLGLEPGENF CMGGPGMIFS REVLRRMVPH IGECLREMYT THEDVEVGRC VRR FGGTQC VWSYEMQQLF HENYEHNRKG YIQDLHNSKI HAAITLHPNK RPAYQYRLHN YMLSRKISEL RYRTIQLHRE SALM SKLSN TEVSKEDQQL GVIPSFNHFQ PRERNEVIEW EFLTGKLLYS AAENQPPRQS LSSILRTALD DTVLQVMEMI NENAK SRGR LIDFKEIQYG YRRVNPMHGV EYILDLLLLY KRHKGRKLTV PVRRHAYLQQ LFSKPFFRET EELDVNSLVE SINSET QSF SFISNSLKIL SSFQGAKEMG GHNEKKVHIL VPLIGRYDIF LRFMENFENM CLIPKQNVKL VIILFSRDSG QDSSKHI EL IKGYQNKYPK AEMTLIPMKG EFSRGLGLEM ASAQFDNDTL LLFCDVDLIF REDFLQRCRD NTIQGQQVYY PIIFSQYD P KVTNGGNPPT DDYFIFSKKT GFWRDYGYGI TCIYKSDLLG AGGFDTSIQG WGLEDVDLYN KVILSGLRPF RSQEVGVVH IFHPVHCDPN LDPKQYKMCL GSKASTFAST MQLAELWLEK HLGVRYNRTL S

UniProtKB: Chondroitin sulfate synthase 3

-
Macromolecule #2: Chondroitin sulfate synthase 2

MacromoleculeName: Chondroitin sulfate synthase 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.06593 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EEPCGPGPPQ PGDSELPPRG NTNAARRPNS VQPGAEREKP GAGEGAGENW EPRVLPYHPA QPGQAAKKAV RTRYISTELG IRQRLLVAV LTSQTTLPTL GVAVNRTLGH RLERVVFLTG ARGRRAPPGM AVVTLGEERP IGHLHLALRH LLEQHGDDFD W FFLVPDTT ...String:
EEPCGPGPPQ PGDSELPPRG NTNAARRPNS VQPGAEREKP GAGEGAGENW EPRVLPYHPA QPGQAAKKAV RTRYISTELG IRQRLLVAV LTSQTTLPTL GVAVNRTLGH RLERVVFLTG ARGRRAPPGM AVVTLGEERP IGHLHLALRH LLEQHGDDFD W FFLVPDTT YTEAHGLARL TGHLSLASAA HLYLGRPQDF IGGEPTPGRY CHGGFGVLLS RMLLQQLRPH LEGCRNDIVS AR PDEWLGR CILDATGVGC TGDHEGVHYS HLELSPGEPV QEGDPHFRSA LTAHPVRDPV HMYQLHKAFA RAELERTYQE IQE LQWEIQ NTSHLAVDGD QAAAWPVGIP APSRPASRFE VLRWDYFTEQ HAFSCADGSP RCPLRGADRA DVADVLGTAL EELN RRYHP ALRLQKQQLV NGYRRFDPAR GMEYTLDLQL EALTPQGGRR PLTRRVQLLR PLSRVEILPV PYVTEASRLT VLLPL AAAE RDLAPGFLEA FATAALEPGD AAAALTLLLL YEPRQAQRVA HADVFAPVKA HVAELERRFP GARVPWLSVQ TAAPSP LRL MDLLSKKHPL DTLFLLAGPD TVLTPDFLNR CRMHAISGWQ AFFPMHFQAF HPAVAPPQGP GPPELGRDTG RFDRQAA SE ACFYNSDYVA ARGRLAAASE QEEELLESLD VYELFLHFSS LHVLRAVEPA LLQRYRAQTC SARLSEDLYH RCLQSVLE G LGSRTQLAML LFEQEQGNST

UniProtKB: Chondroitin sulfate synthase 2

-
Macromolecule #3: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

-
Macromolecule #4: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
GridModel: Quantifoil / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.9 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7000000000000001 µm

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 163527
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

+
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