[English] 日本語
Yorodumi
- EMDB-63448: The hinge-arm region of HBx-Smc5/6 ubiquitination complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63448
TitleThe hinge-arm region of HBx-Smc5/6 ubiquitination complex
Map data
Sample
  • Complex: The hinge-arm region of HBx-Smc5/6 ubiquitination complex
    • Protein or peptide: Structural maintenance of chromosomes protein 6
    • Protein or peptide: Structural maintenance of chromosomes protein 5
KeywordsSmc5/6 / DNA BINDING PROTEIN
Function / homology
Function and homology information


sex chromosome / positive regulation of maintenance of mitotic sister chromatid cohesion / mitotic cell cycle phase transition / positive regulation of chromosome segregation / Smc5-Smc6 complex / DNA secondary structure binding / interchromatin granule / host-mediated suppression of viral genome replication / protein localization to chromosome, centromeric region / chromatin looping ...sex chromosome / positive regulation of maintenance of mitotic sister chromatid cohesion / mitotic cell cycle phase transition / positive regulation of chromosome segregation / Smc5-Smc6 complex / DNA secondary structure binding / interchromatin granule / host-mediated suppression of viral genome replication / protein localization to chromosome, centromeric region / chromatin looping / telomere maintenance via recombination / chromosome condensation / regulation of telomere maintenance / mitotic spindle pole / stem cell population maintenance / protein sumoylation / chromosome, centromeric region / SUMOylation of DNA damage response and repair proteins / chromosome segregation / PML body / double-strand break repair via homologous recombination / cellular senescence / cell junction / single-stranded DNA binding / site of double-strand break / damaged DNA binding / chromosome, telomeric region / nuclear speck / cell division / DNA damage response / ubiquitin protein ligase binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 5 / Structural maintenance of chromosomes protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.32 Å
AuthorsTong C / Lili D / Hongshuai L / Jinhong Z / Qian X / Lanfeng W
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303600 China
CitationJournal: Cell Res / Year: 2026
Title: Structural and functional insights into HBx-Smc6 targeting for HBV inhibition.
Authors: Tong Cheng / Jinhong Zhou / Wenjun Huang / Lili Du / Pengyu He / Renzheng Yang / Yan Gao / Menghan Hao / Kongying Hu / Jieliang Chen / Hongxia Wang / Zihe Rao / Zhenghong Yuan / Lanfeng Wang /
History
DepositionFeb 15, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_63448.png

Downloads & links

-
Map

FileDownload / File: emd_63448.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.)
1.86 Å/pix.
x 256 pix.
= 477.184 Å		1.86 Å/pix.
x 256 pix.
= 477.184 Å		1.86 Å/pix.
x 256 pix.
= 477.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.864 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-3.0076008 - 13.468499
Average (Standard dev.)-0.004743061 (±0.14122725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 477.184 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_63448_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63448_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_63448_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The hinge-arm region of HBx-Smc5/6 ubiquitination complex

EntireName: The hinge-arm region of HBx-Smc5/6 ubiquitination complex
Components
  • Complex: The hinge-arm region of HBx-Smc5/6 ubiquitination complex
    • Protein or peptide: Structural maintenance of chromosomes protein 6
    • Protein or peptide: Structural maintenance of chromosomes protein 5

-
Supramolecule #1: The hinge-arm region of HBx-Smc5/6 ubiquitination complex

SupramoleculeName: The hinge-arm region of HBx-Smc5/6 ubiquitination complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Structural maintenance of chromosomes protein 6

MacromoleculeName: Structural maintenance of chromosomes protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 126.530883 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAKRKEENFS SPKNAKRPRQ EELEDFDKDG DEDECKGTTL TAAEVGIIES IHLKNFMCHS MLGPFKFGSN VNFVVGNNGS GKSAVLTAL IVGLGGRAVA TNRGSSLKGF VKDGQNSADI SITLRNRGDD AFKASVYGNS ILIQQHISID GSRSYKLKSA T GSVVSTRK ...String:
MAKRKEENFS SPKNAKRPRQ EELEDFDKDG DEDECKGTTL TAAEVGIIES IHLKNFMCHS MLGPFKFGSN VNFVVGNNGS GKSAVLTAL IVGLGGRAVA TNRGSSLKGF VKDGQNSADI SITLRNRGDD AFKASVYGNS ILIQQHISID GSRSYKLKSA T GSVVSTRK EELIAILDHF NIQVDNPVSV LTQEMSKQFL QSKNEGDKYK FFMKATQLEQ MKEDYSYIME TKERTKEQIH QG EERLTEL KRQCVEKEER FQSIAGLSTM KTNLESLKHE MAWAVVNEIE KQLNAIRDNI KIGEDRAARL DRKMEEQQVR LNE AEQKYK DIQDKLEKIS EETNARAPEC MALKADVVAK KRAYNEAEVL YNRSLNEYKA LKKDDEQLCK RIEELKKSTD QSLE PERLE RQKKISWLKE RVKAFQNQEN SVNQEIEQFQ QAIEKDKEEH GKIKREELDV KHALSYNQRQ LKELKDSKTD RLKRF GPNV PALLEAIDDA YRQGHFTYKP VGPLGACIHL RDPELALAIE SCLKGLLQAY CCHNHADERV LQALMKRFYL PGTSRP PII VSEFRNEIYD VRHRAAYHPD FPTVLTALEI DNAVVANSLI DMRGIETVLL IKNNSVARAV MQSQKPPKNC REAFTAD GD QVFAGRYYSS ENTRPKFLSR DVDSEISDLE NEVENKTAQI LNLQQHLSAL EKDIKHNEEL LKRCQLHYKE LKMKIRKN I SEIRELENIE EHQSVDIATL EDEAQENKSK MKMVEEHMEQ QKENMEHLKS LKIEAENKYD AIKFKINQLS ELADPLKDE LNLADSEVDN QKRGKRHYEE KQKEHLDTLN KKKRELDMKE KELEEKMSQA RQICPERIEV EKSASILDKE INRLRQKIQA EHASHGDRE EIMRQYQEAR ETYLDLDSKV RTLKKFIKLL GEIMEHRFKT YQQFRRCLTL RCKLYFDNLL SQRAYCGKMN F DHKNETLS ISVQPGEGNK AAFNDMRALS GGERSFSTVC FILSLWSIAE SPFRCLDEFD VYMDMVNRRI AMDLILKMAD SQ RFRQFIL LTPQSMSSLP SSKLIRILRM SDPERGQTTL PFRPVTQEED DDQR

UniProtKB: Structural maintenance of chromosomes protein 6

-
Macromolecule #2: Structural maintenance of chromosomes protein 5

MacromoleculeName: Structural maintenance of chromosomes protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.014594 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MATPSKKTST PSPQPSKRAL PRDPSSEVPS KRKNSAPQLP LLQSSGPFVE GSIVRISMEN FLTYDICEVS PGPHLNMIVG ANGTGKSSI VCAICLGLAG KPAFMGRADK VGFFVKRGCS RGMVEIELFR ASGNLVITRE IDVAKNQSFW FINKKSTTQK I VEEKVAAL ...String:
MATPSKKTST PSPQPSKRAL PRDPSSEVPS KRKNSAPQLP LLQSSGPFVE GSIVRISMEN FLTYDICEVS PGPHLNMIVG ANGTGKSSI VCAICLGLAG KPAFMGRADK VGFFVKRGCS RGMVEIELFR ASGNLVITRE IDVAKNQSFW FINKKSTTQK I VEEKVAAL NIQVGNLCQF LPQDKVGEFA KLSKIELLEA TEKSIGPPEM HKYHCELKNL REKEKQLETS CKEKTEYLQK MV QRNERYK QDVERFYERK RHLDLIEMLE AKRPWVEYEN VRQEYEEVKL VRDRVKEEVR KLKEGQIPVT CRIEEMENER HNL EARIKE KATDIKEASQ KCKQKQDVIE RKDKHIEELQ QALIVKQNEE LDRQRRIGNT RKMIEDLQNE LKTTENCENL QPQI DAITN DLRRIQDEKA LCEGEIIDKR RERETLEKEK KSVDDHIVRF DNLMNQKEDK LRQRFRDTYD AVLWLRNNRD KFKQR VCEP IMLTINMKDN KNAKYIENHI PSNDLRAFVF ESQEDMEVFL KEVRDNKKLR VNAVIAPKSS YADKAPSRSL NELKQY GFF SYLRELFDAP DPVMSYLCCQ YHIHEVPVGT EKTRERIERV IQETRLKQIY TAEEKYVVKT SFYSNKVISS NTSLKVA QF LTVTVDLEQR RHLEEQLKEI HRKLQAVDSG LIALRETSKH LEHKDNELRQ KKKELLERKT KKRQLEQKIS SKLGSLKL M EQDTCNLEEE ERKASTKIKE INVQKAKLVT ELTNLIKICT SLHIQKVDLI LQNTTVISEK NKLESDYMAA SSQLRLTEQ HFIELDENRQ RLLQKCKELM KRARQVCNLG AEQTLPQEYQ TQVPTIPNGH NSSLPMVFQD LPNTLDEIDA LLTEERSRAS CFTGLNPTI VQEYTKREEE IEQLTEELKG KKVELDQYRE NISQVKERWL NPLKELVEKI NEKFSNFFSS MQCAGEVDLH T ENEEDYDK YGIRIRVKFR SSTQLHELTP HHQSGGERSV STMLYLMALQ ELNRCPFRVV DEINQGMDPI NERRVFEMVV NT ACKENTS QYFFITPKLL QNLPYSEKMT VLFVYNGPHM LEPNTWNLKA FQRRRRRITF TQPS

UniProtKB: Structural maintenance of chromosomes protein 5

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 48.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29615
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
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