8D9D

Human DNA polymerase-alpha/primase elongation complex II bound to primer/template


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of human primosome elongation complexes.

He, Q.Baranovskiy, A.G.Morstadt, L.M.Lisova, A.E.Babayeva, N.D.Lusk, B.L.Lim, C.J.Tahirov, T.H.

(2023) Nat Struct Mol Biol 30: 579-583

  • DOI: https://doi.org/10.1038/s41594-023-00971-3
  • Primary Citation of Related Structures:  
    8D96, 8D9D

  • PubMed Abstract: 

    The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. Using cryogenic electron microscopy, we solved a 3.6 Å human primosome structure caught at an early stage of RNA primer elongation with deoxynucleotides. The structure confirms a long-standing role of primase large subunit and reveals new insights into how primosome is limited to synthesizing short RNA-DNA primers.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase small subunit420Homo 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 subunit509Homo 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 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49643
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunit1,462Homo 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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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 
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UniProt GroupQ14181
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3')12Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3')19Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download Ideal Coordinates CCD File 
L [auth C]2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
H [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C],
K [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth C],
M [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

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 StatesR00GM131023
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM127085

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Database references
  • Version 1.3: 2024-06-12
    Changes: Data collection, Refinement description