[English] 日本語
Yorodumi
- EMDB-47110: Cryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47110
TitleCryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex.
Map data
Sample
  • Complex: Double-loaded SUMO E1-E2-SUMO1 complex
    • Protein or peptide: SUMO-conjugating enzyme UBC9
    • Protein or peptide: Small ubiquitin-related modifier 1
    • Protein or peptide: Small ubiquitin-related modifier 1
    • Protein or peptide: SUMO-activating enzyme subunit 1
    • Protein or peptide: SUMO-activating enzyme subunit 2
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: ZINC ION
KeywordsSumo1(a) / Sumo1(t) / sae1 / ubc9 / uba2 / LIGASE
Function / homology
Function and homology information


SUMO activating enzyme activity / SUMO activating enzyme complex / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / negative regulation of potassium ion transmembrane transporter activity / ubiquitin activating enzyme activity / protein localization to nuclear pore / : / transferase complex ...SUMO activating enzyme activity / SUMO activating enzyme complex / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / negative regulation of potassium ion transmembrane transporter activity / ubiquitin activating enzyme activity / protein localization to nuclear pore / : / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of delayed rectifier potassium channel activity / PML body organization / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / nuclear stress granule / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / SUMO binding / positive regulation of protein sumoylation / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / regulation of calcium ion transmembrane transport / ATP-dependent protein binding / Maturation of nucleoprotein / nuclear export / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of protein targeting to mitochondrion / ubiquitin-like protein conjugating enzyme binding / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / transcription factor binding / cellular response to cadmium ion / roof of mouth development / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / nuclear pore / transporter activator activity / negative regulation of DNA-binding transcription factor activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Transcriptional and post-translational regulation of MITF-M expression and activity / Meiotic synapsis / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / chromosome segregation / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / enzyme activator activity / protein tag activity / Formation of Incision Complex in GG-NER / PML body / PKR-mediated signaling / modulation of chemical synaptic transmission / regulation of protein stability / protein modification process / Schaffer collateral - CA1 synapse / nuclear envelope / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / regulation of protein localization / transferase activity / cellular response to heat / ubiquitin-dependent protein catabolic process / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / nuclear speck / nuclear body / positive regulation of cell migration / protein heterodimerization activity / cell division / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus
Similarity search - Function
SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Small ubiquitin-related modifier 1, Ubl domain / Ubiquitin/SUMO-activating enzyme E1-like ...SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Small ubiquitin-related modifier 1, Ubl domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Small ubiquitin-related modifier 1 / SUMO-conjugating enzyme UBC9 / SUMO-activating enzyme subunit 1 / SUMO-activating enzyme subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsJia L / Nayak D / Ruben EA / Nayak A / Wasmuth EV / Olsen SK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex.
Authors: Jia L / Nayak D / Ruben EA / Nayak A / Wasmuth EV / Olsen SK
History
DepositionSep 23, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47110.png

Downloads & links

-
Map

FileDownload / File: emd_47110.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.)
0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-0.57131517 - 0.91119117
Average (Standard dev.)0.0001664105 (±0.02159713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 222.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_47110_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_47110_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_47110_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Double-loaded SUMO E1-E2-SUMO1 complex

EntireName: Double-loaded SUMO E1-E2-SUMO1 complex
Components
  • Complex: Double-loaded SUMO E1-E2-SUMO1 complex
    • Protein or peptide: SUMO-conjugating enzyme UBC9
    • Protein or peptide: Small ubiquitin-related modifier 1
    • Protein or peptide: Small ubiquitin-related modifier 1
    • Protein or peptide: SUMO-activating enzyme subunit 1
    • Protein or peptide: SUMO-activating enzyme subunit 2
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: ZINC ION

-
Supramolecule #1: Double-loaded SUMO E1-E2-SUMO1 complex

SupramoleculeName: Double-loaded SUMO E1-E2-SUMO1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: SUMO-conjugating enzyme UBC9

MacromoleculeName: SUMO-conjugating enzyme UBC9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.255172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MSGIALSRLA QERKAWRKDH PAQFSAVPTK NPDGTMNLMN WECAIPGKKG TPWEGGLFKL RMLFKDDYP SSPPKCKFEP PLFHPNVYPS GTVCLSILEE DKDWRPAITI KQILLGIQEL LNEPNIQDPK QAEAYTIYSQ N RVEYEKRV RAQARKFAPS

UniProtKB: SUMO-conjugating enzyme UBC9

-
Macromolecule #2: Small ubiquitin-related modifier 1

MacromoleculeName: Small ubiquitin-related modifier 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.320909 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MSDQEAKPST EDLGDKKEGE YIKLKVIGQD SSEIHFKVKM TTHLKKLKES YCQRQGVPMN SLRFLFEGQ RIADNHTPKE LGMEEEDVIE VYQEQTGG

UniProtKB: Small ubiquitin-related modifier 1

-
Macromolecule #3: Small ubiquitin-related modifier 1

MacromoleculeName: Small ubiquitin-related modifier 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.288844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MSDQEAKPST EDLGDKKEGE YIKLKVIGQD SSEIHFKVKM TTHLKKLKES YAQRQGVPMN SLRFLFEGQ RIADNHTPKE LGMEEEDVIE VYQEQTGG

UniProtKB: Small ubiquitin-related modifier 1

-
Macromolecule #4: SUMO-activating enzyme subunit 1

MacromoleculeName: SUMO-activating enzyme subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.671137 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MVEKEEAGGG ISEEEAAQYD RQIRLWGLEA QKRLRASRVL LVGLKGLGAE IAKNLILAGV KGLTMLDHE QVTPEDPGAQ FLIRTGSVGR NRAEASLERA QNLNPMVDVK VDTEDIEKKP ESFFTQFDAV CLTCCSRDVI V KVDQICHK ...String:
MGSSHHHHHH SSGLVPRGSH MVEKEEAGGG ISEEEAAQYD RQIRLWGLEA QKRLRASRVL LVGLKGLGAE IAKNLILAGV KGLTMLDHE QVTPEDPGAQ FLIRTGSVGR NRAEASLERA QNLNPMVDVK VDTEDIEKKP ESFFTQFDAV CLTCCSRDVI V KVDQICHK NSIKFFTGDV FGYHGYTFAN LGEHEFVEEK TKVAKVSQGV EDGPDTKRAK LDSSETTMVK KKVVFCPVKE AL EVDWSSE KAKAALKRTT SDYFLLQVLL KFRTDKGRDP SSDTYEEDSE LLLQIRNDVL DSLGISPDLL PEDFVRYCFS EMA PVCAVV GGILAQEIVK ALSQRDPPHN NFFFFDGMKG NGIVECLGPK

UniProtKB: SUMO-activating enzyme subunit 1

-
Macromolecule #5: SUMO-activating enzyme subunit 2

MacromoleculeName: SUMO-activating enzyme subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.230844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALSRGLPRE LAEAVAGGRV LVVGAGGIGC ELLKNLVLTG FSHIDLIDLD TIDVSNLNRQ FLFQKKHVGR SKAQVAKESV LQFYPKANI VAYHDSIMNP DYNVEFFRQF ILVMNALDNR AARNHVNRMC LAADVPLIES GTAGYLGQVT TIKKGVTECY E CHPKPTQR ...String:
MALSRGLPRE LAEAVAGGRV LVVGAGGIGC ELLKNLVLTG FSHIDLIDLD TIDVSNLNRQ FLFQKKHVGR SKAQVAKESV LQFYPKANI VAYHDSIMNP DYNVEFFRQF ILVMNALDNR AARNHVNRMC LAADVPLIES GTAGYLGQVT TIKKGVTECY E CHPKPTQR TFPGCTIRNT PSEPIHCIVW AKYLFNQLFG EEDADQEVSP DRADPEAAWE PTEAEARARA SNEDGDIKRI ST KEWAKST GYDPVKLFTK LFKDDIRYLL TMDKLWRKRK PPVPLDWAEV QSQGEETNAS DQQNEPQLGL KDQQVLDVKS YAR LFSKSI ETLRVHLAEK GDGAELIWDK DDPSAMDFVT SAANLRMHIF SMNMKSRFDI KSMAGNIIPA IATTNAVIAG LIVL EGLKI LSGKIDQCRT IFLNKQPNPR KKLLVPCALD PPNPNCYVCA SKPEVTVRLN VHKVTVLTLQ DKIVKEKFAM VAPDV QIED GKGTILISSE EGETEANNHK KLSEFGIRNG SRLQADDFLQ DYTLLINILH SEDLGKDVEF EVVG

UniProtKB: SUMO-activating enzyme subunit 2

-
Macromolecule #6: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

-
Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3kyc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113479
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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