8D9D

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

PDB DOI: https://doi.org/10.2210/pdb8D9D/pdb
EM Map EMD-27258: EMDB EMDataResource
NAKB: 8D9D

Classification: REPLICATION
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, Spodoptera frugiperda
Mutation(s): No

Deposited: 2022-06-09 Released: 2023-04-19
Deposition Author(s): He, Q., Baranovskiy, A., Lim, C., Tahirov, T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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

PubMed: 37069376 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 334.97 kDa
Atom Count: 19,409
Modelled Residue Count: 2,343
Deposited Residue Count: 2,866
Unique protein chains: 4
Unique nucleic acid chains: 1
Unique hybrid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase small subunit	A	420	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49642
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase large subunit	B	509	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49643
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase alpha catalytic subunit	C	1,462	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09884
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Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14181
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-D((GTP))-R(PGPCPGPGPCPAPCPG)-D(PAPCPC)-3')	E	12	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (5'-D(APTPGPGPTPCPGPTPGPCPCPGPCPCPAPAPTPAP*A)-3')	F	19	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTP Query on DTP Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ SUYVUBYJARFZHO-RRKCRQDMSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C]	G [auth A], J [auth C], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth C] Focus chain K [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain M [auth E] MOL2 format, chain I [auth C] MOL2 format, chain M [auth E] mmCIF format, chain I [auth C] mmCIF format, chain M [auth E]	I [auth C], M [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain M [auth E] Interactions & Density Focus chain I [auth C] Focus chain M [auth E]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2023-04-19

Deposition Author(s):

Funding Organization	Location	Grant Number
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	R35GM127085