RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Gene Name = "PRIM2"

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 19 Structures.

Refinements

Structure Determination Methodology

experimental (19)

Scientific Name of Source Organism

	Homo sapiens (19)
	Severe acute respiratory syndrome-related coronavirus (1)

Taxonomy

	Eukaryota (19)
	Riboviria (1)

Experimental Method

	ELECTRON MICROSCOPY (10)
	X-RAY DIFFRACTION (9)

Polymer Entity Type

	Protein (19)
	DNA (8)
	NA-hybrid (2)
	RNA (2)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (3)
	2.5 - 3.0 (3)
	3.0 - 3.5 (6)
	3.5 - 4.0 (2)
	4.0 - 4.5 (2)
	> 4.5 (1)

Release Date

	2010 - 2014 (2)
	2015 - 2019 (7)
	2020 - 2024 (10)

Enzyme Classification Name

	Transferases (19)
	Hydrolases (1)

Symmetry Type

	Asymmetric (16)
	Cyclic (4)

AllSelected

1 to 19 of 19 Structures

Page 1 of 1

Sort by

Explore in 3D

3L9Q \| pdb_00003l9q	Download File View File

Crystal structure of human polymerase alpha-primase p58 iron-sulfur cluster domain

Vaithiyalingam, S., Eichman, B.F., Chazin, W.J.

(2010) Proc Natl Acad Sci U S A 107: 13684-13689

Released	2010-07-14
Method	X-RAY DIFFRACTION 1.698 Å
Organisms	Homo sapiens
Macromolecule	DNA primase large subunit (protein)
Unique Ligands	SF4, SO4

Explore in 3D

3Q36 \| pdb_00003q36	Download File View File

Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit

Agarkar, V.B., Babayeva, N.D., Tahirov, T.H.

(2011) Cell Cycle 10: 926-931

Released	2011-04-13
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	DNA primase large subunit (protein)
Unique Ligands	FE, SF4

Explore in 3D

4RR2 \| pdb_00004rr2	Download File View File

Crystal structure of human primase

Baranovskiy, A.G., Gu, J., Suwa, Y., Babayeva, N.D., Tahirov, T.H.

(2015) J Biological Chem 290: 5635-5646

Released	2015-01-21
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	DNA primase large subunit (protein) DNA primase small subunit (protein)
Unique Ligands	SF4, ZN

Explore in 3D

5DQO \| pdb_00005dqo	Download File View File

Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain

Salay, L.E., Thompson, M.K., Chazin, W.J.

(2017) Science 355:

Released	2016-09-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	DNA primase large subunit (protein)
Unique Ligands	SF4

Explore in 3D

5EXR \| pdb_00005exr	Download File View File

Crystal structure of human primosome

Tahirov, T.H., Baranovskiy, A.G., Babayeva, N.D.

(2016) J Biological Chem 291: 10006-10020

Released	2016-03-23
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase alpha catalytic subunit (protein) DNA polymerase alpha subunit B (protein) DNA primase large subunit (protein) DNA primase small subunit (protein)
Unique Ligands	SF4, ZN

Explore in 3D

5F0Q \| pdb_00005f0q	Download File View File

Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer

Tahirov, T.H., Baranovskiy, A.G., Babayeva, N.D.

(2016) J Biological Chem 291: 10006-10020

Released	2016-03-23
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	Homo sapiens
Macromolecule	DNA primase large subunit (protein) DNA (5'-D(GPCPCPGPCPCPAPAPCPAPTPA)-3') (nucleic acid) RNA (5'-R(PGPGPCPGPGPC)-3') (nucleic acid)
Unique Ligands	MG, SF4

Explore in 3D

5F0S \| pdb_00005f0s	Download File View File

Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer and manganese ion

Tahirov, T.H., Baranovskiy, A.G., Babayeva, N.D.

(2016) J Biological Chem 291: 10006-10020

Released	2016-03-23
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	DNA primase large subunit (protein) DNA (5'-D(GPCPCPGPCPCPAPAPCPAPTPA)-3') (nucleic acid) RNA (5'-R(PGPGPCPGPGPC)-3') (nucleic acid)
Unique Ligands	MN, SF4

Explore in 3D

5I7M \| pdb_00005i7m	Download File View File

Crystal structure of Y345F mutant of human primase p58 iron-sulfur cluster domain

Salay, L.E., Thompson, M.K., Chazin, W.J.

(2017) Science 355:

Released	2017-03-01
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Homo sapiens
Macromolecule	DNA primase large subunit (protein)
Unique Ligands	SF4, SO4

Explore in 3D

6DHW \| pdb_00006dhw	Download File View File

Crystal structure of primase iron-sulfur domain (266-457)

Holt, M.E., Salay, L.E., Chazin, W.J.

(2018) PLoS One 13: e0209345-e0209345

Released	2018-12-19
Method	X-RAY DIFFRACTION 2.013 Å
Organisms	Homo sapiens
Macromolecule	DNA primase large subunit (protein)
Unique Ligands	SF4, SO4

Explore in 3D

7OPL \| pdb_00007opl	Download File View File

CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1

Kilkenny, M.L., Pellegrini, L.

(2022) Protein Sci 31: 333-344

Released	2021-11-10
Method	ELECTRON MICROSCOPY 4.12 Å
Organisms	Homo sapiens Severe acute respiratory syndrome-related coronavirus
Macromolecule	DNA polymerase alpha catalytic subunit (protein) DNA polymerase alpha subunit B (protein) DNA primase large subunit (protein) DNA primase small subunit (protein) Non-structural protein 1 (protein)
Unique Ligands	SF4, ZN

Explore in 3D

7U5C \| pdb_00007u5c	Download File View File

Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state

Cai, S.W., Zinder, J.C., Svetlov, V., Bush, M.W., Nudler, E., Walz, T., de Lange, T.

(2022) Nat Struct Mol Biol 29: 813-819

Released	2022-05-18
Method	ELECTRON MICROSCOPY 4.6 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 1
Unique Ligands	SF4, ZN

Explore in 3D

8B9D \| pdb_00008b9d	Download File View File

Human replisome bound by Pol Alpha

Jones, M.L., Yeeles, J.T.P.

(2023) Mol Cell 83: 2911

Released	2023-08-09
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 19 Unique nucleic acid chains: 2
Unique Ligands	ANP, MG, ZN

Explore in 3D

8D0B \| pdb_00008d0b	Download File View File

Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template

He, Q., Lin, X., Chavez, B.L., Agrawal, S., Lusk, B.L., Lim, C.

(2022) Nature 608: 826-832

Released	2022-06-22
Method	ELECTRON MICROSCOPY 3.43 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 1

Explore in 3D

8D0K \| pdb_00008d0k	Download File View File

Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template - PRIM2C advanced PIC

He, Q., Lin, X., Chavez, B.L., Agrawal, S., Lusk, B.L., Lim, C.

(2022) Nature 608: 826-832

Released	2022-06-22
Method	ELECTRON MICROSCOPY 4.27 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 1

Explore in 3D

8D96 \| pdb_00008d96	Download File View File

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

He, Q., Baranovskiy, A., Lim, C., Tahirov, T.

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

Released	2023-04-19
Method	ELECTRON MICROSCOPY 3.35 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase alpha catalytic subunit (protein) DNA primase large subunit (protein) DNA (5'-D(APTPAPAPTPGPGPTPCPGPTPGPCPCPGPCPCPAPAPTPAPA)-3') (nucleic acid) DNA/RNA (5'-GTP)-R(PGPCPGPGPCPAPCPG)-D(PAPCP*C)-3') (hybrid)
Unique Ligands	DTP, MG, SF4

Explore in 3D

8D9D \| pdb_00008d9d	Download File View File

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

He, Q., Baranovskiy, A., Lim, C., Tahirov, T.

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

Released	2023-04-19
Method	ELECTRON MICROSCOPY 3.59 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 1 Unique nucleic acid hybrid chains: 1
Unique Ligands	DTP, MG, SF4, ZN

Explore in 3D

8QJ7 \| pdb_00008qj7	Download File View File

Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1

Yin, Z., Pellegrini, L.

(2024) FEBS J 291: 1813-1829

Released	2024-02-21
Method	ELECTRON MICROSCOPY 3.07 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase alpha catalytic subunit (protein) DNA polymerase alpha subunit B (protein) DNA primase large subunit (protein) DNA primase small subunit (protein)
Unique Ligands	ATP, MN, SF4, ZN

Explore in 3D

8VY3 \| pdb_00008vy3	Download File View File

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

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

(2024) Nat Commun 15: 7705-7705

Released	2024-09-04
Method	ELECTRON MICROSCOPY 2.98 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase alpha catalytic subunit (protein) DNA polymerase alpha subunit B (protein) DNA primase large subunit (protein) DNA primase small subunit (protein)
Unique Ligands	SF4, ZN

Explore in 3D

9C8V \| pdb_00009c8v	Download File View File

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

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

(2024) Nat Commun 15: 7705-7705

Released	2024-09-04
Method	ELECTRON MICROSCOPY 3.39 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase alpha catalytic subunit (protein) DNA polymerase alpha subunit B (protein) DNA primase large subunit (protein) DNA primase small subunit (protein)
Unique Ligands	SF4, ZN

1 to 19 of 19 Structures

Page 1 of 1

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

3L9Q | pdb_00003l9q

Crystal structure of human polymerase alpha-primase p58 iron-sulfur cluster domain

3Q36 | pdb_00003q36

Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit

4RR2 | pdb_00004rr2

Crystal structure of human primase

5DQO | pdb_00005dqo

Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain

5EXR | pdb_00005exr

Crystal structure of human primosome

5F0Q | pdb_00005f0q

Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer

5F0S | pdb_00005f0s

Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer and manganese ion

5I7M | pdb_00005i7m

Crystal structure of Y345F mutant of human primase p58 iron-sulfur cluster domain

6DHW | pdb_00006dhw

Crystal structure of primase iron-sulfur domain (266-457)

7OPL | pdb_00007opl

CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1

7U5C | pdb_00007u5c

Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state

8B9D | pdb_00008b9d

Human replisome bound by Pol Alpha

8D0B | pdb_00008d0b

Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template

8D0K | pdb_00008d0k

Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template - PRIM2C advanced PIC

8D96 | pdb_00008d96

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

8D9D | pdb_00008d9d

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

8QJ7 | pdb_00008qj7

Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1

8VY3 | pdb_00008vy3

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

9C8V | pdb_00009c8v

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

3L9Q | pdb_00003l9q

3Q36 | pdb_00003q36

4RR2 | pdb_00004rr2

5DQO | pdb_00005dqo

5EXR | pdb_00005exr

5F0Q | pdb_00005f0q

5F0S | pdb_00005f0s

5I7M | pdb_00005i7m

6DHW | pdb_00006dhw

7OPL | pdb_00007opl

7U5C | pdb_00007u5c

8B9D | pdb_00008b9d

8D0B | pdb_00008d0b

8D0K | pdb_00008d0k

8D96 | pdb_00008d96

8D9D | pdb_00008d9d

8QJ7 | pdb_00008qj7

8VY3 | pdb_00008vy3

9C8V | pdb_00009c8v