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

235,183 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: Expression Organism = "in vitro transcription vector pT7-Fluc(deltai)"

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 47 Structures.

Refinements

Structure Determination Methodology

experimental (47)

Scientific Name of Source Organism

	Homo sapiens (13)
	Tetrahymena (13)
	Brome mosaic virus (4)
	Brussowvirus bv2972 (4)
	Methanocaldococcus jannaschii (4)
	Streptococcus phage D1811 (4)
	Phaseolus vulgaris (3)
	Streptococcus thermophilus (3)
	Geobacter (2)
	Human immunodeficiency virus 1 (2)

More...

Taxonomy

	Eukaryota (32)
	Bacteria (10)
	Riboviria (9)
	Archaea (4)
	Duplodnaviria (4)

Experimental Method

	ELECTRON MICROSCOPY (27)
	X-RAY DIFFRACTION (17)
	SOLUTION NMR (3)

Polymer Entity Type

	RNA (46)
	Protein (19)
	DNA (4)
	NA-hybrid (1)

Refinement Resolution (Å)

	2.0 - 2.5 (6)
	2.5 - 3.0 (14)
	3.0 - 3.5 (15)
	3.5 - 4.0 (5)
	4.0 - 4.5 (2)
	> 4.5 (2)

Release Date

	2015 - 2019 (18)
	2020 - 2024 (25)
	2025 - 2029 (4)

Enzyme Classification Name

	Transferases (4)
	Hydrolases (6)
	Ligases (4)

Symmetry Type

	Asymmetric (15)
	Cyclic (4)

SCOP Classification

	Alpha and beta proteins (a+b) (2)
	Artifacts (1)
	Peptides (1)

AllSelected

1 to 25 of 47 Structures

Page 1 of 2

Sort by

Explore in 3D

4YAZ \| pdb_00004yaz	Download File View File

3',3'-cGAMP riboswitch bound with 3',3'-cGAMP

Ren, A.M., Patel, D.J., Rajashankar, R.K.

(2015) Cell Rep 11: 1-12

Released	2015-04-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Geobacter
Macromolecule	RNA (84-MER) (nucleic acid)
Unique Ligands	4BW, K, MG

Explore in 3D

4YB0 \| pdb_00004yb0	Download File View File

3',3'-cGAMP riboswitch bound with c-di-GMP

Ren, A.M., Patel, D.J., Rajashankar, R.K.

(2015) Cell Rep 11: 1-12

Released	2015-04-15
Method	X-RAY DIFFRACTION 2.121 Å
Organisms	Geobacter
Macromolecule	RNA (84-MER) (nucleic acid)
Unique Ligands	C2E, GDP, K, MG

Explore in 3D

4YB1 \| pdb_00004yb1	Download File View File

20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP

Ren, A.M., Patel, D.J., Rajashankar, R.K.

(2015) Cell Rep 11: 1-12

Released	2015-04-15
Method	X-RAY DIFFRACTION 2.081 Å
Organisms	Homo sapiens Vibrio cholerae
Macromolecule	U1 small nuclear ribonucleoprotein A (protein) RNA (91-MER) (nucleic acid)
Unique Ligands	4BW, MG

Explore in 3D

5J0M \| pdb_00005j0m	Download File View File

Ground state sampled during RDC restrained Replica-averaged Metadynamics (RAM) simulations of the HIV-1 TAR complexed with cyclic peptide mimetic of Tat

Borkar, A.N., Bardaro Jr., M.F., Varani, G., Vendruscolo, M.

(2016) Proc Natl Acad Sci U S A 113: 7171-7176

Released	2016-06-08
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	Cyclic peptide mimetic of HIV-1 Tat (protein) Apical region (29-mer) of the HIV-1 TAR RNA element (nucleic acid)

Explore in 3D

5J2W \| pdb_00005j2w	Download File View File

Intermediate state lying on the pathway of release of Tat from HIV-1 TAR.

Borkar, A.N., Bardaro Jr., M.F., Varani, G., Vendruscolo, M.

(2016) Proc Natl Acad Sci U S A 113: 7171-7176

Released	2016-06-08
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	Cyclic peptide mimetic of HIV-1 Tat (protein) Apical region (29mer) of the HIV-1 TAR RNA element (nucleic acid)

Explore in 3D

5MPS \| pdb_00005mps	Download File View File

Structure of a spliceosome remodeled for exon ligation

Fica, S.M., Oubridge, C., Galej, W.P., Wilkinson, M.E., Newman, A.J., Bai, X.-C., Nagai, K.

(2017) Nature 542: 377-380

Released	2017-01-18
Method	ELECTRON MICROSCOPY 3.85 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 25 Unique nucleic acid chains: 5
Unique Ligands	GTP, IHP, K, MG, ZN

Explore in 3D

5MQ0 \| pdb_00005mq0	Download File View File

Structure of a spliceosome remodeled for exon ligation

Fica, S.M., Oubridge, C., Galej, W.P., Wilkinson, M.E., Newman, A.J., Bai, X.-C., Nagai, K.

(2017) Nature 542: 377-380

Released	2017-01-18
Method	ELECTRON MICROSCOPY 4.17 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 30 Unique nucleic acid chains: 6
Unique Ligands	GTP, IHP, K, MG, ZN

Explore in 3D

6N5K \| pdb_00006n5k	Download File View File

Structure of Human pir-miRNA-449c Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

Shoffner, G.M., Peng, Z., Guo, F.

To be published

Released	2019-11-27
Method	X-RAY DIFFRACTION 3.098 Å
Organisms	Homo sapiens
Macromolecule	RNA (125-MER) (nucleic acid)
Unique Ligands	2BA, K, MG, SO4

Explore in 3D

6N5N \| pdb_00006n5n	Download File View File

Structure of Human pir-miRNA-208a Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

Shoffner, G.M., Peng, Z., Guo, F.

To be published

Released	2019-11-27
Method	X-RAY DIFFRACTION 2.951 Å
Organisms	Homo sapiens
Macromolecule	RNA (125-MER) (nucleic acid)
Unique Ligands	2BA, K, MG, SO4

Explore in 3D

6N5O \| pdb_00006n5o	Download File View File

Structure of Human pir-miRNA-202 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

Shoffner, G.M., Peng, Z., Guo, F.

To be published

Released	2019-11-27
Method	X-RAY DIFFRACTION 2.708 Å
Organisms	Homo sapiens
Macromolecule	RNA (126-MER) (nucleic acid)
Unique Ligands	2BA, K, MG, SO4

Explore in 3D

6N5P \| pdb_00006n5p	Download File View File

Structure of Human pir-miRNA-340 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

Shoffner, G.M., Peng, Z., Guo, F.

To be published

Released	2019-11-27
Method	X-RAY DIFFRACTION 2.991 Å
Organisms	Homo sapiens
Macromolecule	RNA (127-MER) (nucleic acid)
Unique Ligands	2BA, K, MG, SO4

Explore in 3D

6N5Q \| pdb_00006n5q	Download File View File

Structure of Human pir-miRNA-378a Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

Shoffner, G.M., Peng, Z., Guo, F.

To be published

Released	2019-11-27
Method	X-RAY DIFFRACTION 2.946 Å
Organisms	Homo sapiens
Macromolecule	RNA (128-MER) (nucleic acid)
Unique Ligands	2BA, K, MG, SO4

Explore in 3D

6N5S \| pdb_00006n5s	Download File View File

Structure of Human pir-miRNA-320b-2 Apical Loop and One-base-pair Stem Fused to the YdaO Riboswitch Scaffold

Shoffner, G.M., Peng, Z., Guo, F.

To be published

Released	2019-11-27
Method	X-RAY DIFFRACTION 2.802 Å
Organisms	Homo sapiens
Macromolecule	RNA (123-MER) (nucleic acid)
Unique Ligands	2BA, 5GP, K, MG, SO4

Explore in 3D

6N5T \| pdb_00006n5t	Download File View File

Structure of Human pir-miRNA-378a Apical Loop Fused to the YdaO Riboswitch Scaffold

Shoffner, G.M., Peng, Z., Guo, F.

To be published

Released	2019-11-27
Method	X-RAY DIFFRACTION 2.787 Å
Organisms	Homo sapiens
Macromolecule	RNA (126-MER) (nucleic acid)
Unique Ligands	2BA, K, MG, SO4

Explore in 3D

6RJ9 \| pdb_00006rj9	Download File View File

Cryo-EM structure of St1Cas9-sgRNA-tDNA20-AcrIIA6 monomeric assembly.

Goulet, A., Chaves-Sanjuan, A., Cambillau, C.

(2019) Mol Cell 76: 922

Released	2019-10-02
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Brussowvirus bv2972 Streptococcus phage D1811 Streptococcus thermophilus Streptococcus thermophilus LMD-9
Macromolecule	AcrIIA6 (protein) CRISPR-associated endonuclease Cas9 1 (protein) sgRNA (nucleic acid) tDNA20 (nucleic acid)

Explore in 3D

6RJA \| pdb_00006rja	Download File View File

Cryo-EM structure of St1Cas9-sgRNA-tDNA20-AcrIIA6 dimeric assembly.

Goulet, A., Cambillau, C., Chaves-Sanjuan, A.

(2019) Mol Cell 76: 922

Released	2019-10-02
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Brussowvirus bv2972 Streptococcus phage D1811 Streptococcus thermophilus Streptococcus thermophilus LMD-9
Macromolecule	AcrIIA6 (protein) CRISPR-associated endonuclease Cas9 1 (protein) RNA (78-MER) (nucleic acid) tDNA20 (nucleic acid)

Explore in 3D

6RJD \| pdb_00006rjd	Download File View File

Cryo-EM structure of St1Cas9-sgRNA-tDNA59-ntPAM complex.

Goulet, A., Chaves-Sanjuan, A., Cambillau, C.

(2019) Mol Cell 76: 922

Released	2019-10-02
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Brussowvirus bv2972 Streptococcus phage D1811 Streptococcus thermophilus DGCC 7710
Macromolecule	Streptococcus Thermophilus 1 Cas9 (protein) ntPAM (nucleic acid) sgRNA (78-MER) (nucleic acid) tDNA59 (nucleic acid)

Explore in 3D

6RJG \| pdb_00006rjg	Download File View File

Cryo-EM structure of St1Cas9-sgRNA-AcrIIA6-tDNA59-ntPAM complex.

Goulet, A., Chaves-Sanjuan, A., Cambillau, C.

(2019) Mol Cell 76: 922

Released	2019-10-02
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Brussowvirus bv2972 Streptococcus phage D1811 Streptococcus thermophilus Streptococcus thermophilus DGCC 7710
Macromolecule	AcrIIA6 (protein) Cas 9 (protein) ntPAM (nucleic acid) sgRNA (nucleic acid) tDNA59 (nucleic acid)

Explore in 3D

6SNJ \| pdb_00006snj	Download File View File

Solution structure of the FUS/TLS RNA recognition motif in complex with U1 snRNA stem loop III

Campagne, S., Allain, F.H.

(2020) Nat Commun 11: 6341-6341

Released	2020-10-28
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	RNA-binding protein FUS (protein) U1 snRNA stem loop III, RNA (28-MER) (nucleic acid)

Explore in 3D

6WTL \| pdb_00006wtl	Download File View File

Structure of Human pir-miRNA-19b-2 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold

Shoffner, G.M., Peng, Z., Guo, F.

To be published

Released	2021-05-05
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	RNA (124-MER) (nucleic acid)
Unique Ligands	2BA, K, MG, SO4

Explore in 3D

6WTR \| pdb_00006wtr	Download File View File

Structure of Human pir-miRNA-300 Apical Loop Fused to the YdaO Riboswitch Scaffold

Shoffner, G.M., Peng, Z., Guo, F.

To be published

Released	2021-05-05
Method	X-RAY DIFFRACTION 3.082 Å
Organisms	Homo sapiens
Macromolecule	RNA (125-MER) (nucleic acid)
Unique Ligands	2BA, K, MG, SO4

Explore in 3D

7KJT \| pdb_00007kjt	Download File View File

KEOPS tRNA modifying sub-complex of archaeal Cgi121 and tRNA

Ceccarelli, D.F., Beenstock, J., Mao, D.Y.L., Sicheri, F.

(2020) Nat Commun 11: 6233-6233

Released	2020-12-02
Method	X-RAY DIFFRACTION 3.34 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Regulatory protein Cgi121 (protein) RNA (70-MER) (nucleic acid)

Explore in 3D

7KJU \| pdb_00007kju	Download File View File

Cgi121-tRNA complex

Ceccarelli, D.F., Beenstock, J., Wan, L.C.K., Sicheri, F.

(2020) Nat Commun 11: 6233-6233

Released	2020-12-02
Method	X-RAY DIFFRACTION 3.102 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	RNA (75-MER) (nucleic acid)
Unique Ligands	MG

Explore in 3D

7MLX \| pdb_00007mlx	Download File View File

SARS-CoV-2 programmed -1 frameshifting element three stem H-type pseudoknot

Roman, C., Lewicka, A.

(2021) ACS Chem Biol 16: 1469-1481

Released	2021-08-11
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	BL3-6 Fab Heavy Chain (protein) BL3-6 Fab Light Chain (protein) RNA (65-MER) (nucleic acid)

Explore in 3D

7RGU \| pdb_00007rgu	Download File View File

The crystal structure of RocC bound to a transcriptional terminator

Kim, H.J., Edwards, R.A., Glover, J.N.M.

(2022) Nat Commun 13: 7076-7076

Released	2022-11-09
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Legionella pneumophila
Macromolecule	Repressor of competence, RNA Chaperone (protein) Modified SL3 of RocR (nucleic acid)

1 to 25 of 47 Structures

Page 1 of 2

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.

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

SCOP Classification

4YAZ | pdb_00004yaz

4YB0 | pdb_00004yb0

4YB1 | pdb_00004yb1

5J0M | pdb_00005j0m

5J2W | pdb_00005j2w

5MPS | pdb_00005mps

5MQ0 | pdb_00005mq0

6N5K | pdb_00006n5k

6N5N | pdb_00006n5n

6N5O | pdb_00006n5o

6N5P | pdb_00006n5p

6N5Q | pdb_00006n5q

6N5S | pdb_00006n5s

6N5T | pdb_00006n5t

6RJ9 | pdb_00006rj9

6RJA | pdb_00006rja

6RJD | pdb_00006rjd

6RJG | pdb_00006rjg

6SNJ | pdb_00006snj

6WTL | pdb_00006wtl

6WTR | pdb_00006wtr

7KJT | pdb_00007kjt

7KJU | pdb_00007kju

7MLX | pdb_00007mlx

7RGU | pdb_00007rgu