[English] 日本語
Yorodumi
- EMDB-37634: SR protein kinase 2 bound at 2-fold vertex of Hepatitis B virus capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37634
TitleSR protein kinase 2 bound at 2-fold vertex of Hepatitis B virus capsid
Map data
Sample
  • Complex: Hepatitis B virus capsid in complex with SR protein kinase 2
    • Complex: SR protein kinase 2
      • Protein or peptide: SR protein kinase 2
    • Complex: Hepatitis B virus capsid
      • Protein or peptide: Hepatitis B virus core protein
KeywordsViral core capsid / Icosahedral / Kinase / Complex / SPLICING
Biological speciesHomo sapiens (human) / Hepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsYip RPH / Lai LTF / Kwok DCY / Lau WCY / Ngo JCK
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)14177317 Hong Kong
CitationJournal: PLoS Pathog / Year: 2024
Title: SRPK2 Mediates HBV Core Protein Phosphorylation and Capsid Assembly via Docking Interaction.
Authors: Ryan Pak Hong Yip / Doris Ching Ying Kwok / Louis Tung Faat Lai / Siu-Ming Ho / Ivan Chun Kit Wong / Chi-Ping Chan / Wilson Chun Yu Lau / Jacky Chi Ki Ngo /
Abstract: Members of the serine-arginine protein kinase (SRPK) family, SRPK1 and SRPK2, phosphorylate the hepatitis B core protein (Cp) and are crucial for pregenomic RNA encapsidation during viral ...Members of the serine-arginine protein kinase (SRPK) family, SRPK1 and SRPK2, phosphorylate the hepatitis B core protein (Cp) and are crucial for pregenomic RNA encapsidation during viral nucleocapsid assembly. Among them, SRPK2 exhibits higher kinase activity toward Cp. In this study, we identified Cp sites that are phosphorylated by SRPK2 and demonstrated that the kinase utilizes an SRPK-specific docking groove to interact with and regulate the phosphorylation of the C-terminal arginine rich domain of Cp. We determined that direct interaction between the docking groove of SRPK2 and unphosphorylated Cp inhibited premature viral capsid assembly in vitro, whereas the phosphorylation of the viral protein reactivated the process. Pull-down assays together with the new cryo-electron microscopy structure of the HBV capsid in complex with SRPK2 revealed that the kinases decorate the surface of the viral capsid by interacting with the C-terminal domain of Cp, underscoring the importance of the docking interaction in regulating capsid assembly and pregenome packaging. Moreover, SRPK2-knockout in HepG2 cells suppressed Cp phosphorylation, indicating that SRPK2 is an important cellular kinase for HBV life cycle.
History
DepositionOct 1, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37634.png

Downloads & links

-
Map

FileDownload / File: emd_37634.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.938 Å
Density
Contour LevelBy AUTHOR: 0.0257
Minimum - Maximum-0.0471264 - 0.123757534
Average (Standard dev.)-0.0002811646 (±0.0035000248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 496.128 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_37634_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37634_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_37634_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Hepatitis B virus capsid in complex with SR protein kinase 2

EntireName: Hepatitis B virus capsid in complex with SR protein kinase 2
Components
  • Complex: Hepatitis B virus capsid in complex with SR protein kinase 2
    • Complex: SR protein kinase 2
      • Protein or peptide: SR protein kinase 2
    • Complex: Hepatitis B virus capsid
      • Protein or peptide: Hepatitis B virus core protein

-
Supramolecule #1: Hepatitis B virus capsid in complex with SR protein kinase 2

SupramoleculeName: Hepatitis B virus capsid in complex with SR protein kinase 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52 kDa/nm

-
Supramolecule #2: SR protein kinase 2

SupramoleculeName: SR protein kinase 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Hepatitis B virus

-
Supramolecule #3: Hepatitis B virus capsid

SupramoleculeName: Hepatitis B virus capsid / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

-
Macromolecule #1: SR protein kinase 2

MacromoleculeName: SR protein kinase 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH NMSVNSEKSS SSERPEPQQK APLVPPPPPP PPPPPPPLPD PTPPEPEEEI LGSDDEEQED PADYCKGGYH PVKIGDLFNG RYHVIRKLGW GHFSTVWLCW DMQGKRFVAM KVVKSAQHYT ETALDEIKLL KCVRESDPSD PNKDMVVQLI ...String:
MGSSHHHHHH SSGLVPRGSH NMSVNSEKSS SSERPEPQQK APLVPPPPPP PPPPPPPLPD PTPPEPEEEI LGSDDEEQED PADYCKGGYH PVKIGDLFNG RYHVIRKLGW GHFSTVWLCW DMQGKRFVAM KVVKSAQHYT ETALDEIKLL KCVRESDPSD PNKDMVVQLI DDFKISGMNG IHVCMVFEVL GHHLLKWIIK SNYQGLPVRC VKSIIRQVLQ GLDYLHSKCK IIHTDIKPEN ILMCVDDAYV RRMAAEATEW QKAGAPPPSG SAVSTAPRAA DLLVNPLDPR NADKIRVKIA DLGNACWVHK HFTEDIQTRQ YRSIEVLIGA GYSTPADIWS TACMAFELAT GDYLFEPHSG EDYSRDEDHI AHIIELLGSI PRHFALSGKY SREFFNRRGE LRHITKLKPW SLFDVLVEKY GWPHEDAAQF TDFLIPMLEM VPEKRASAGE CLRHPWLNS

-
Macromolecule #2: Hepatitis B virus core protein

MacromoleculeName: Hepatitis B virus core protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGNNLEDPA SRDLVVNYVN TNMGLKIRQL LWFHISCLTF GRETVLEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVR ...String:
MGSSHHHHHH SSGLVPRGSH MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGNNLEDPA SRDLVVNYVN TNMGLKIRQL LWFHISCLTF GRETVLEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVR RRDRGRSPRR RTPSPRRRRS QSPRRRRSQS RESQC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.9 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS TALOS F200C
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 824 / Average exposure time: 54.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 54774
Startup modelType of model: EMDB MAP
EMDB ID:

3015

Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1.2)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.1.2)
Details: A number of 6266 refined particles of the whole complex were symmetry expanded with icosahedral symmetry, followed by particle subtraction using a reference mask covering the asymmetric ...Details: A number of 6266 refined particles of the whole complex were symmetry expanded with icosahedral symmetry, followed by particle subtraction using a reference mask covering the asymmetric subparticles without centering. A masked classification of the asymmetric subparticles was operated with C1 symmetry, regularization parameter T=40 and local angular search.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 58259
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