9C8V

Human DNA polymerase alpha/primase - CHAPSO (4 mM)

• PDB DOI: https://doi.org/10.2210/pdb9C8V/pdb
• EM Map EMD-43627: EMDB EMDataResource

• Classification: REPLICATION
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-06-13 Released: 2024-09-04 
• Deposition Author(s): Abe, K.M., Li, G., He, Q., Grant, T., Lim, C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Human DNA polymerase alpha/primase - CHAPSO (4 mM)

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 277.62 kDa 
• Atom Count: 18,829 
• Modelled Residue Count: 2,324 
• Deposited Residue Count: 2,409 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase small subunit	A	412	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase large subunit	B	434	Homo sapiens	Mutation(s): 0  Gene Names: PRIM2, PRIM2A
UniProt & NIH Common Fund Data Resources
Find proteins for P49643 (Homo sapiens) Explore P49643  Go to UniProtKB:  P49643
PHAROS:  P49643 GTEx:  ENSG00000146143

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase alpha catalytic subunit	C	1,119	Homo sapiens	Mutation(s): 0  Gene Names: POLA1, POLA 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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase alpha subunit B	D	444	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	F [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN	E [auth A], G [auth C], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Abe, K.M., Li, G., He, Q., Grant, T., Lim, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM130550
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R00GM131023
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2GM150023

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release