+Open data
-Basic information
Entry | Database: PDB / ID: 8hm0 | ||||||
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Title | F8-A22-E4 complex of MPXV in trimeric form | ||||||
Components |
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Keywords | REPLICATION / MPXV / complex / RECOMBINATION | ||||||
Function / homology | Function and homology information viral DNA genome replication / uracil DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA recombination / DNA replication / DNA-directed DNA polymerase ...viral DNA genome replication / uracil DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA recombination / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Monkeypox virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Li, Y.N. / Shen, Y.P. / Hu, Z.W. / Yan, R.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2023 Title: Structural basis for the assembly of the DNA polymerase holoenzyme from a monkeypox virus variant. Authors: Yaning Li / Yaping Shen / Ziwei Hu / Renhong Yan / Abstract: The ongoing global pandemic caused by a variant of the monkeypox (or mpox) virus (MPXV) has prompted widespread concern. The MPXV DNA polymerase holoenzyme, consisting of F8, A22, and E4, is vital ...The ongoing global pandemic caused by a variant of the monkeypox (or mpox) virus (MPXV) has prompted widespread concern. The MPXV DNA polymerase holoenzyme, consisting of F8, A22, and E4, is vital for replicating the viral genome and represents a crucial target for the development of antiviral drugs. However, the assembly and working mechanism for the DNA polymerase holoenzyme of MPXV remains elusive. Here, we present the cryo-electron microscopy (cryo-EM) structure of the DNA polymerase holoenzyme at an overall resolution of 3.5 Å. Unexpectedly, the holoenzyme is assembled as a dimer of heterotrimers, of which the extra interface between the thumb domain of F8 and A22 shows a clash between A22 and substrate DNA, suggesting an autoinhibition state. Addition of exogenous double-stranded DNA shifts the hexamer into trimer exposing DNA binding sites, potentially representing a more active state. Our findings provide crucial steps toward developing targeted antiviral therapies for MPXV and related viruses. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hm0.cif.gz | 269.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hm0.ent.gz | 209 KB | Display | PDB format |
PDBx/mmJSON format | 8hm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hm0_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8hm0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8hm0_validation.xml.gz | 49.4 KB | Display | |
Data in CIF | 8hm0_validation.cif.gz | 74 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/8hm0 ftp://data.pdbj.org/pub/pdb/validation_reports/hm/8hm0 | HTTPS FTP |
-Related structure data
Related structure data | 34887MC 8hlzC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 49203.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus Gene: A22R, MPXV-COP-126, MPXV-M2940_FCT-131, MPXV-M2957_Lagos-131, MPXV-M3021_Delta-131, MPXV-M5320_M15_Bayelsa-124, MPXV-Nig_SEV71_2_82-126, MPXV-PCH-128, MPXV-Singapore-131, MPXV-SL-126, MPXV-UK_ ...Gene: A22R, MPXV-COP-126, MPXV-M2940_FCT-131, MPXV-M2957_Lagos-131, MPXV-M3021_Delta-131, MPXV-M5320_M15_Bayelsa-124, MPXV-Nig_SEV71_2_82-126, MPXV-PCH-128, MPXV-Singapore-131, MPXV-SL-126, MPXV-UK_P1-131, MPXV-UK_P2-131, MPXV-UK_P3-131, MPXV-USA2003_099_GR-131, MPXV-USA2003_206_DM-131, MPXV-USA2003_223_RS-131, MPXV-UTC-122, MPXV-W_Nigeria-126, MPXV-WRAIR126, MPXV297957_122, MPXV298464_113, MPXV_LIB1970_184_138, MPXV_USA2003_039_138, MPXV_USA2003_044_138, PDLMKLCO_00135 Production host: Homo sapiens (human) / References: UniProt: Q5IXP2 |
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#2: Protein | Mass: 117147.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus Gene: POL, MPXV-M2940_FCT-055, MPXV-M2957_Lagos-055, MPXV-M3021_Delta-055, MPXV-M5320_M15_Bayelsa-048, MPXV-Singapore-055, MPXV-UK_P1-055, MPXV-UK_P2-055, MPXV-UK_P3-055, MPXV298464_038, PDLMKLCO_00060 Production host: Homo sapiens (human) References: UniProt: A0A2L0AR76, DNA-directed DNA polymerase |
#3: Protein | Mass: 25107.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus Gene: E4R, UNG, MPXV-CAM1990_02-093, MPXV-Congo_8-094, MPXV-COP-095, MPXV-GAB1988_001-094, MPXV-Ikubi-093, MPXV-M2940_FCT-099, MPXV-M2957_Lagos-099, MPXV-M3021_Delta-099, MPXV-M5320_M15_Bayelsa-092, ...Gene: E4R, UNG, MPXV-CAM1990_02-093, MPXV-Congo_8-094, MPXV-COP-095, MPXV-GAB1988_001-094, MPXV-Ikubi-093, MPXV-M2940_FCT-099, MPXV-M2957_Lagos-099, MPXV-M3021_Delta-099, MPXV-M5320_M15_Bayelsa-092, MPXV-Nig_SEV71_2_82-094, MPXV-PCH-096, MPXV-Singapore-099, MPXV-SL-095, MPXV-UK_P1-099, MPXV-UK_P2-099, MPXV-UK_P3-099, MPXV-USA2003_099_GR-099, MPXV-USA2003_206_DM-099, MPXV-USA2003_223_RS-099, MPXV-UTC-090, MPXV-W_Nigeria-094, MPXV-WRAIR095, MPXV297957_090, MPXV298464_081, MPXV_DRC_Yandongi_102, MPXV_LIB1970_184_106, MPXV_RCG2003_358_106, MPXV_SUD2005_01_102, MPXV_USA2003_039_106, MPXV_USA2003_044_106, MPXV_ZAI1979_005_106, MPXVgp101, PDLMKLCO_00104 Production host: Homo sapiens (human) / References: UniProt: Q5IXS4, uracil-DNA glycosylase |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1400 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: RELION / Version: 3.0.6 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 854700 / Symmetry type: POINT |