8VY3 | pdb_00008vy3

Human DNA polymerase alpha/primase - AavLEA1 (1:40 molar ratio)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe, K.M.Li, G.He, Q.Grant, T.Lim, C.J.

(2024) Nat Commun 15: 7705-7705

  • DOI: https://doi.org/10.1038/s41467-024-52091-1
  • Primary Citation of Related Structures:  
    8VY3, 9C8U, 9C8V

  • PubMed Abstract: 

    Air-water interface (AWI) interactions during cryo-electron microscopy (cryo-EM) sample preparation cause significant sample loss, hindering structural biology research. Organisms like nematodes and tardigrades produce Late Embryogenesis Abundant (LEA) proteins to withstand desiccation stress. Here we show that these LEA proteins, when used as additives during plunge freezing, effectively mitigate AWI damage to fragile multi-subunit molecular samples. The resulting high-resolution cryo-EM maps are comparable to or better than those obtained using existing AWI damage mitigation methods. Cryogenic electron tomography reveals that particles are localized at specific interfaces, suggesting LEA proteins form a barrier at the AWI. This interaction may explain the observed sample-dependent preferred orientation of particles. LEA proteins offer a simple, cost-effective, and adaptable approach for cryo-EM structural biologists to overcome AWI-related sample damage, potentially revitalizing challenging projects and advancing the field of structural biology.


  • Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase small subunit412Homo sapiensMutation(s): 0 
Gene Names: PRIM1
EC: 2.7.7.102
UniProt & NIH Common Fund Data Resources
Find proteins for P49642 (Homo sapiens)
Explore P49642 
Go to UniProtKB:  P49642
PHAROS:  P49642
GTEx:  ENSG00000198056 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49642
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunit434Homo sapiensMutation(s): 0 
Gene Names: PRIM2PRIM2A
UniProt & NIH Common Fund Data Resources
Find proteins for P49643 (Homo sapiens)
Explore P49643 
Go to UniProtKB:  P49643
PHAROS:  P49643
GTEx:  ENSG00000146143 
Entity Groups  
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UniProt GroupP49643
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunit1,119Homo sapiensMutation(s): 0 
Gene Names: POLA1POLA
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for P09884 (Homo sapiens)
Explore P09884 
Go to UniProtKB:  P09884
PHAROS:  P09884
GTEx:  ENSG00000101868 
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UniProt GroupP09884
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha subunit B444Homo sapiensMutation(s): 0 
Gene Names: POLA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14181 (Homo sapiens)
Explore Q14181 
Go to UniProtKB:  Q14181
PHAROS:  Q14181
GTEx:  ENSG00000014138 
Entity Groups  
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UniProt GroupQ14181
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM130550
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR00GM131023
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2GM150023

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references, Structure summary