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: Citation Author = "Gootenberg, J.S."

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 14 Structures.

Refinements

Structure Determination Methodology

experimental (14)

Scientific Name of Source Organism

	Desulfonema ishimotonii (6)
	synthetic construct (6)
	Francisella tularensis subsp. novicida (3)
	Francisella tularensis subsp. novicida U112 (3)
	Campylobacter jejuni (2)
	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 (2)
	Corynebacterium diphtheriae (1)
	Corynebacterium diphtheriae NCTC 13129 (1)
	Escherichia coli (1)
	Segatella buccae (1)

More...

Taxonomy

	Bacteria (14)
	other sequences (6)

Experimental Method

	X-RAY DIFFRACTION (8)
	ELECTRON MICROSCOPY (6)

Polymer Entity Type

	Protein (14)
	RNA (13)
	DNA (7)
	NA-hybrid (1)

Refinement Resolution (Å)

	1.5 - 2.0 (4)
	2.0 - 2.5 (4)
	2.5 - 3.0 (6)

Release Date

	2015 - 2019 (8)
	2020 - 2024 (6)

Enzyme Classification Name

Hydrolases (6)

Symmetry Type

Asymmetric (14)

AllSelected

1 to 14 of 14 Structures

Page 1 of 1

Sort by

Explore in 3D

5B2O \| pdb_00005b2o	Download File View File

Crystal structure of Francisella novicida Cas9 in complex with sgRNA and target DNA (TGG PAM)

Hirano, H., Nishimasu, H., Nakane, T., Ishitani, R., Nureki, O.

(2016) Cell 164: 950-961

Released	2016-03-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Francisella tularensis subsp. novicida Francisella tularensis subsp. novicida U112 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) DNA (5'-D(TPGPGPTPAPTPCPGP*G)-3') (nucleic acid) Guide RNA (nucleic acid) Target DNA (nucleic acid)
Unique Ligands	ACT, CA, CL, EDO, NA, ZN

Explore in 3D

5B2P \| pdb_00005b2p	Download File View File

Crystal structure of Francisella novicida Cas9 in complex with sgRNA and target DNA (TGA PAM)

Hirano, H., Nishimasu, H., Nakane, T., Ishitani, R., Nureki, O.

(2016) Cell 164: 950-961

Released	2016-03-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Francisella tularensis subsp. novicida Francisella tularensis subsp. novicida U112 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) DNA (5'-D(TPGPAPTPAPTPCPGP*G)-3') (nucleic acid) Target DNA (nucleic acid) Guide RNA (hybrid)
Unique Ligands	ACT, CA, CL, EDO, NA, ZN

Explore in 3D

5B2Q \| pdb_00005b2q	Download File View File

Crystal structure of Francisella novicida Cas9 RHA in complex with sgRNA and target DNA (TGG PAM)

Hirano, H., Nishimasu, H., Nakane, T., Ishitani, R., Nureki, O.

(2016) Cell 164: 950-961

Released	2016-03-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Francisella tularensis subsp. novicida Francisella tularensis subsp. novicida U112 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) DNA (5'-D(TPGPGPTPAPTPCPGP*G)-3') (nucleic acid) Guide RNA (nucleic acid) Target DNA (nucleic acid)
Unique Ligands	ACT, CA, CL, EDO, NA, ZN

Explore in 3D

5X2G \| pdb_00005x2g	Download File View File

Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACC PAM)

Yamada, M., Watanabe, Y., Hirano, H., Nakane, T., Ishitani, R., Nishimasu, H., Nureki, O.

(2017) Mol Cell 65: 1109-1121.e3

Released	2017-03-29
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Campylobacter jejuni Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) Non-target DNA strand (nucleic acid) Target DNA strand (nucleic acid) sgRNA (nucleic acid)
Unique Ligands	EDO

Explore in 3D

5X2H \| pdb_00005x2h	Download File View File

Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACA PAM)

Yamada, M., Watanabe, Y., Hirano, H., Nakane, T., Ishitani, R., Nishimasu, H., Nureki, O.

(2017) Mol Cell 65: 1109-1121.e3

Released	2017-03-29
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Campylobacter jejuni Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) Non-target DNA strand (nucleic acid) Target DNA strand (nucleic acid) sgRNA (nucleic acid)
Unique Ligands	EDO

Explore in 3D

6AI6 \| pdb_00006ai6	Download File View File

Crystal structure of SpCas9-NG

Nishimasu, H., Hirano, S., Ishitani, R., Nureki, O.

(2018) Science 361: 1259-1262

Released	2018-10-31
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Streptococcus pyogenes Streptococcus pyogenes serotype M1
Macromolecule	CRISPR-associated endonuclease Cas9/Csn1 (protein) DNA (28-MER) (nucleic acid) DNA (8-MER) (nucleic acid) RNA (81-MER) (nucleic acid)
Unique Ligands	EDO, K, MG

Explore in 3D

6DTD \| pdb_00006dtd	Download File View File

High-resolution crystal structure of Cas13b from Prevotella buccae

Slaymaker, I.M.S., Zhang, F.Z.

(2019) Cell Rep 26: 3741-3751.e5

Released	2019-02-20
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Segatella buccae
Macromolecule	nuclease (protein) RNA (37-MER) (nucleic acid)
Unique Ligands	CIT, CL, NA, PG4

Explore in 3D

6JOO \| pdb_00006joo	Download File View File

Crystal structure of Corynebacterium diphtheriae Cas9 in complex with sgRNA and target DNA

Hirano, S., Ishitani, R., Nishimasu, H., Nureki, O.

(2019) Nat Commun 10: 1968-1968

Released	2019-04-17
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Corynebacterium diphtheriae Corynebacterium diphtheriae NCTC 13129
Macromolecule	CRISPR-associated protein,CRISPR-associated endonuclease Cas9 (protein) Guide RNA (nucleic acid) Non-Target DNA (nucleic acid) Target DNA (nucleic acid)
Unique Ligands	EDO, ZN

Explore in 3D

7WAH \| pdb_00007wah	Download File View File

Structure of Cas7-11 in complex with guide RNA and target RNA

Kato, K., Okazaki, S., Isayama, Y., Nishizawa, T., Nishimasu, H.

(2022) Cell 185: 2324-2337.e16

Released	2022-06-15
Method	ELECTRON MICROSCOPY 2.45 Å
Organisms	Desulfonema ishimotonii Escherichia coli
Macromolecule	CRISPR-associated RAMP family protein (protein) crRNA (39-MER) (nucleic acid) tgRNA (5'-R(PUPAPCPCPCPAPUPGPUPCPGPAPAPGPAPCPAPAPCPAPAPAP*G)-3') (nucleic acid)
Unique Ligands	ZN

Explore in 3D

7Y9X \| pdb_00007y9x	Download File View File

Structure of the Cas7-11-Csx29-guide RNA complex

Kato, K., Okazaki, S., Ishikawa, J., Isayama, Y., Nishizawa, T., Nishimasu, H.

(2022) Science 378: 882-889

Released	2022-11-09
Method	ELECTRON MICROSCOPY 2.49 Å
Organisms	Desulfonema ishimotonii
Macromolecule	CHAT domain-containing protein (protein) CRISPR-associated RAMP family protein (protein) crRNA (nucleic acid)
Unique Ligands	ZN

Explore in 3D

7Y9Y \| pdb_00007y9y	Download File View File

Structure of the Cas7-11-Csx29-guide RNA-target RNA (no PFS) complex

Kato, K., Okazaki, S., Ishikawa, J., Isayama, Y., Nishizawa, T., Nishimasu, H.

(2022) Science 378: 882-889

Released	2022-11-09
Method	ELECTRON MICROSCOPY 2.77 Å
Organisms	Desulfonema ishimotonii
Macromolecule	CHAT domain-containing protein (protein) CRISPR-associated RAMP family protein (protein) RNA (27-MER) (nucleic acid) RNA (38-MER) (nucleic acid)
Unique Ligands	ZN

Explore in 3D

8EEX \| pdb_00008eex	Download File View File

Cas7-11 in complex with Csx29

Demircioglu, F.E., Wilkinson, M.E., Strecker, J., Li, D., Faure, G., Macrae, R.K., Zhang, F.

(2022) Science 378: 874-881

Released	2022-11-16
Method	ELECTRON MICROSCOPY 2.95 Å
Organisms	Desulfonema ishimotonii
Macromolecule	Cas7-11 (protein) Csx29 (protein) crRNA (nucleic acid)
Unique Ligands	ZN

Explore in 3D

8EEY \| pdb_00008eey	Download File View File

Cas7-11 in complex with DR-mismatched target RNA, Csx29 and Csx30

Demircioglu, F.E., Wilkinson, M.E., Strecker, J., Li, D., Faure, G., Macrae, R.K., Zhang, F.

(2022) Science 378: 874-881

Released	2022-11-16
Method	ELECTRON MICROSCOPY 2.53 Å
Organisms	Desulfonema ishimotonii synthetic construct
Macromolecule	Cas7-11 (protein) Csx29 (protein) Csx30 (protein) DR-mismatched target RNA (nucleic acid) crRNA (nucleic acid)
Unique Ligands	ZN

Explore in 3D

8GS2 \| pdb_00008gs2	Download File View File

Structure of the Cas7-11-Csx29-guide RNA-target RNA (non-matching PFS) complex

Kato, K., Okazaki, S., Ishikawa, J., Isayama, Y., Nishizawa, T., Nishimasu, H.

(2022) Science 378: 882-889

Released	2022-11-09
Method	ELECTRON MICROSCOPY 2.84 Å
Organisms	Desulfonema ishimotonii
Macromolecule	CHAT domain-containing protein (protein) CRISPR-associated RAMP family protein (protein) crRNA (nucleic acid) target RNA with non-matching PFS (nucleic acid)
Unique Ligands	AMP, C5P, ZN

1 to 14 of 14 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.

5B2O | pdb_00005b2o

Crystal structure of Francisella novicida Cas9 in complex with sgRNA and target DNA (TGG PAM)

5B2P | pdb_00005b2p

Crystal structure of Francisella novicida Cas9 in complex with sgRNA and target DNA (TGA PAM)

5B2Q | pdb_00005b2q

Crystal structure of Francisella novicida Cas9 RHA in complex with sgRNA and target DNA (TGG PAM)

5X2G | pdb_00005x2g

Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACC PAM)

5X2H | pdb_00005x2h

Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACA PAM)

6AI6 | pdb_00006ai6

Crystal structure of SpCas9-NG

6DTD | pdb_00006dtd

High-resolution crystal structure of Cas13b from Prevotella buccae

6JOO | pdb_00006joo

Crystal structure of Corynebacterium diphtheriae Cas9 in complex with sgRNA and target DNA

7WAH | pdb_00007wah

Structure of Cas7-11 in complex with guide RNA and target RNA

7Y9X | pdb_00007y9x

Structure of the Cas7-11-Csx29-guide RNA complex

7Y9Y | pdb_00007y9y

Structure of the Cas7-11-Csx29-guide RNA-target RNA (no PFS) complex

8EEX | pdb_00008eex

Cas7-11 in complex with Csx29

8EEY | pdb_00008eey

Cas7-11 in complex with DR-mismatched target RNA, Csx29 and Csx30

8GS2 | pdb_00008gs2

Structure of the Cas7-11-Csx29-guide RNA-target RNA (non-matching PFS) complex

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

5B2O | pdb_00005b2o

5B2P | pdb_00005b2p

5B2Q | pdb_00005b2q

5X2G | pdb_00005x2g

5X2H | pdb_00005x2h

6AI6 | pdb_00006ai6

6DTD | pdb_00006dtd

6JOO | pdb_00006joo

7WAH | pdb_00007wah

7Y9X | pdb_00007y9x

7Y9Y | pdb_00007y9y

8EEX | pdb_00008eex

8EEY | pdb_00008eey

8GS2 | pdb_00008gs2