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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Source Organism Taxonomy Name (Full Lineage) = "Acidaminococcus"

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Search Summary

This query matches 24 Structures.

Refinements

Structure Determination Methodology

experimental (24)

Scientific Name of Source Organism

	Acidaminococcus sp. BV3L6 (16)
	synthetic construct (12)
	Acidaminococcus fermentans (4)
	Acidaminococcus fermentans DSM 20731 (3)
	Acidaminococcus (1)
	Acidaminococcus intestini (1)

Taxonomy

	Bacteria (24)
	other sequences (12)

Experimental Method

	ELECTRON MICROSCOPY (12)
	X-RAY DIFFRACTION (12)

Polymer Entity Type

	Protein (24)
	DNA (16)
	RNA (16)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (4)
	2.0 - 2.5 (3)
	2.5 - 3.0 (2)
	3.0 - 3.5 (7)
	3.5 - 4.0 (7)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (2)
	2005 - 2009 (1)
	2010 - 2014 (4)
	2015 - 2019 (4)
	2020 - 2024 (9)
	2025 - 2029 (3)

Enzyme Classification Name

	Hydrolases (17)
	Lyases (17)
	Transferases (1)
	Oxidoreductases (1)
	Translocases (1)

Symmetry Type

	Asymmetric (19)
	Cyclic (4)
	Dihedral (4)

SCOP Classification

	Alpha and beta proteins (a/b) (6)
	All alpha proteins (1)
	Alpha and beta proteins (a+b) (1)
	Artifacts (1)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 24 of 24 Structures

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1HUX \| pdb_00001hux	Download File View File

CRYSTAL STRUCTURE OF THE ACIDAMINOCOCCUS FERMENTANS (R)-2-HYDROXYGLUTARYL-COA DEHYDRATASE COMPONENT A

Locher, K.P., Hans, M., Yeh, A.P., Schmid, B., Buckel, W., Rees, D.C.

(2001) J Mol Biology 307: 297-308

Released	2001-03-21
Method	X-RAY DIFFRACTION 3 Å
Organisms	Acidaminococcus fermentans
Macromolecule	ACTIVATOR OF (R)-2-HYDROXYGLUTARYL-COA DEHYDRATASE (protein)
Unique Ligands	ADP, SF4

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1PIX \| pdb_00001pix	Download File View File

Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase

Wendt, K.S., Schall, I., Huber, R., Buckel, W., Jacob, U.

(2003) EMBO J 22: 3493-3502

Released	2003-08-05
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Acidaminococcus fermentans
Macromolecule	Glutaconyl-CoA decarboxylase A subunit (protein)
Unique Ligands	FMT, SO4

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1POI \| pdb_00001poi	Download File View File

CRYSTAL STRUCTURE OF GLUTACONATE COENZYME A-TRANSFERASE FROM ACIDAMINOCOCCUS FERMENTANS TO 2.55 ANGSTOMS RESOLUTION

Jacob, U., Mack, M., Clausen, T., Huber, R., Buckel, W., Messerschmidt, A.

(1997) Structure 5: 415-426

Released	1998-03-18
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Acidaminococcus fermentans
Macromolecule	GLUTACONATE COENZYME A-TRANSFERASE (protein)
Unique Ligands	CU

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1XDW \| pdb_00001xdw	Download File View File

NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans

Martins, B.M., Macedo-Ribeiro, S., Bresser, J., Buckel, W., Messerschmidt, A.

(2005) FEBS J 272: 269-281

Released	2005-03-08
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Acidaminococcus fermentans
Macromolecule	NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase (protein)

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4HYR \| pdb_00004hyr	Download File View File

Structure of putative Glucarate dehydratase from Acidaminococcus sp. D21 with unusual static disorder

Hegde, R.P., Toro, R., Burley, S.K., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

To be published

Released	2013-02-13
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Acidaminococcus intestini
Macromolecule	Glucarate dehydratase (protein)
Unique Ligands	CL, EDO, GOL

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4KPU \| pdb_00004kpu	Download File View File

Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a mechanism of flavin-based electron bifurcation

Mowafy, A.M., Chowdhury, N.P., Demmer, J., Upadhyay, V., Kolzer, S., Jayamani, E., Kahnt, J., Demmer, U., Ermler, U., Buckel, W.

(2014) J Biological Chem 289: 5145-5157

Released	2014-01-15
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Acidaminococcus fermentans DSM 20731
Macromolecule	Electron transfer flavoprotein alpha subunit (protein) Electron transfer flavoprotein alpha/beta-subunit (protein)
Unique Ligands	CL, FAD

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4L1F \| pdb_00004l1f	Download File View File

Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a mechanism of flavin-based electron bifurcation

Mowafy, A.M., Chowdhury, N.P., Demmer, J., Upadhyay, V., Kolzer, S., Jayamani, E., Kahnt, J., Demmer, U., Ermler, U., Buckel, W.

(2014) J Biological Chem 289: 5145-5157

Released	2014-01-15
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Acidaminococcus fermentans DSM 20731
Macromolecule	Acyl-CoA dehydrogenase domain protein (protein)
Unique Ligands	COS, FAD, NA, PDO, PO4

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4L2I \| pdb_00004l2i	Download File View File

Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a mechanism of flavin-based electron bifurcation

Mowafy, A.M., Chowdhury, N.P., Demmer, J., Upadhyay, V., Kolzer, S., Jayamani, E., Kahnt, J., Demmer, U., Ermler, U., Buckel, W.

(2014) J Biological Chem 289: 5145-5157

Released	2014-01-15
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Acidaminococcus fermentans DSM 20731
Macromolecule	Electron transfer flavoprotein alpha subunit (protein) Electron transfer flavoprotein alpha/beta-subunit (protein)
Unique Ligands	CL, FAD, NAD

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5B43 \| pdb_00005b43	Download File View File

Crystal structure of Acidaminococcus sp. Cpf1 in complex with crRNA and target DNA

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

(2016) Cell 165: 949-962

Released	2016-05-04
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Acidaminococcus Acidaminococcus sp. BV3L6
Macromolecule	CRISPR-associated endonuclease Cpf1 (protein) DNA (34-MER) (nucleic acid) DNA (5'-D(CPAPGPTPCPCPTPTPTPA)-3') (nucleic acid) RNA (43-MER) (nucleic acid)
Unique Ligands	EDO, NA

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5KK5 \| pdb_00005kk5	Download File View File

AsCpf1(E993A)-crRNA-DNA ternary complex

Gao, P., Yang, H., Rajashankar, K.R., Huang, Z., Patel, D.J.

(2016) Cell Res 26: 901-913

Released	2016-08-10
Method	X-RAY DIFFRACTION 3.289 Å
Organisms	Acidaminococcus sp. BV3L6
Macromolecule	CRISPR-associated endonuclease Cpf1 (protein) DNA (28-MER) (nucleic acid) DNA (8-mer) (nucleic acid) RNA (40-MER) (nucleic acid)

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5XH6 \| pdb_00005xh6	Download File View File

Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with crRNA and target DNA (TATA PAM)

Nishimasu, H., Yamano, T., Ishitani, R., Nureki, O.

(2017) Mol Cell 67: 139-147.e2

Released	2017-06-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Acidaminococcus sp. BV3L6
Macromolecule	CRISPR-associated endonuclease Cpf1 (protein) Non-target DNA strand (nucleic acid) Target DNA strand (nucleic acid) crRNA (nucleic acid)
Unique Ligands	CL, EDO, NA

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5XH7 \| pdb_00005xh7	Download File View File

Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RR variant in complex with crRNA and target DNA (TCCA PAM)

Nishimasu, H., Yamano, T., Ishitani, R., Nureki, O.

(2017) Mol Cell 67: 139-147.e2

Released	2017-06-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Acidaminococcus sp. BV3L6
Macromolecule	CRISPR-associated endonuclease Cpf1 (protein) Non-target DNA strand (nucleic acid) Target DNA strand (nucleic acid) crRNA (nucleic acid)
Unique Ligands	CL, EDO, NA

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8SFH \| pdb_00008sfh	Download File View File

WT CRISPR-Cas12a with a 5bp R-loop

Strohkendl, I., Taylor, D.W.

(2024) Mol Cell 84: 2717-2731.e6

Released	2024-07-03
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) DNA (32-MER) (nucleic acid) RNA (27-MER) (nucleic acid)

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8SFI \| pdb_00008sfi	Download File View File

WT CRISPR-Cas12a with a 8bp R-loop

Strohkendl, I., Taylor, D.W.

(2024) Mol Cell 84: 2717-2731.e6

Released	2024-07-03
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) DNA (5'-D(PCPTPTPAPTPCPAPCPTPAPAPAPAPGPAPTPCPGPGPAPAPG)-3') (nucleic acid) DNA (5'-D(PCPTPTPCPCPGPAPTPCPTPTPTPTPAPGPTPGPAPTPA)-3') (nucleic acid) RNA (28-MER) (nucleic acid)

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8SFJ \| pdb_00008sfj	Download File View File

WT CRISPR-Cas12a with a 10bp R-loop

Strohkendl, I., Taylor, D.W.

(2024) Mol Cell 84: 2717-2731.e6

Released	2024-07-03
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) DNA (5'-D(PCPAPCPTPTPAPTPCPAPCPTPAPAPAPAPGPAPTPCPGPGPAPAPG)-3') (nucleic acid) DNA (5'-D(PCPTPTPCPCPGPAPTPCPTPTPTPTPAPGPTPGPAP*T)-3') (nucleic acid) RNA (29-MER) (nucleic acid)

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8SFL \| pdb_00008sfl	Download File View File

WT CRISPR-Cas12a with a 15bp R-loop

Strohkendl, I., Taylor, D.W.

(2024) Mol Cell 84: 2717-2731.e6

Released	2024-07-03
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) DNA (40-MER) (nucleic acid) RNA (34-MER) (nucleic acid)

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8SFN \| pdb_00008sfn	Download File View File

WT CRISPR-Cas12a with a 16bp R-loop and nontarget strand in the RuvC active site.

Strohkendl, I., Taylor, D.W.

(2024) Mol Cell 84: 2717-2731.e6

Released	2024-07-03
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) DNA (30-MER) (nucleic acid) DNA (31-MER) (nucleic acid) RNA (36-MER) (nucleic acid)

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8SFO \| pdb_00008sfo	Download File View File

WT CRISPR-Cas12a with a 20bp R-loop and nontarget strand in the RuvC active site.

Strohkendl, I., Taylor, D.W.

(2024) Mol Cell 84: 2717-2731.e6

Released	2024-07-03
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) DNA (35-MER) (nucleic acid) DNA (40-MER) (nucleic acid) RNA (39-MER) (nucleic acid)
Unique Ligands	MG

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8SFP \| pdb_00008sfp	Download File View File

WT CRISPR-Cas12a with the target strand in the RuvC active site.

Strohkendl, I., Taylor, D.W.

(2024) Mol Cell 84: 2717-2731.e6

Released	2024-07-03
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) DNA (40-MER) (nucleic acid) DNA (5'-D(PCPTPTPCPCPGPAPTPCPTPTPTPTPAPGPTPGPAPTPA)-3') (nucleic acid) RNA (39-MER) (nucleic acid)

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8SFQ \| pdb_00008sfq	Download File View File

WT CRISPR-Cas12a post nontarget strand-cleavage with the the RuvC active site exposed.

Strohkendl, I., Taylor, D.W.

(2024) Mol Cell 84: 2717-2731.e6

Released	2024-07-03
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) DNA (34-MER) (nucleic acid) DNA (5'-D(PCPTPTPCPCPGPAPTPCPTPTPTPTPAPGPTPGPAP*T)-3') (nucleic acid) RNA (39-MER) (nucleic acid)

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8SFR \| pdb_00008sfr	Download File View File

WT CRISPR-Cas12a post nontarget strand cleavage.

Strohkendl, I., Taylor, D.W.

(2024) Mol Cell 84: 2717-2731.e6

Released	2024-07-03
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) DNA (34-MER) (nucleic acid) DNA (5'-D(PCPTPTPCPCPGPAPTPCPTPTPTPTPAPGPTPGPAP*T)-3') (nucleic acid) RNA (39-MER) (nucleic acid)

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9CJH \| pdb_00009cjh	Download File View File

Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs, structure 1

Soczek, K.M., Doudna, J.A.

(2025) Nucleic Acids Res 53:

Released	2025-01-08
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) Non-target DNA strand (nucleic acid) Target DNA strand (nucleic acid) guide RNA (25-MER) (nucleic acid)

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9CJI \| pdb_00009cji	Download File View File

Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs, structure 2

Soczek, K.M., Doudna, J.A.

(2025) Nucleic Acids Res 53:

Released	2025-01-08
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) Non-target DNA strand (nucleic acid) Target DNA strand (nucleic acid) guide RNA (25-MER) (nucleic acid)

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9CJJ \| pdb_00009cjj	Download File View File

Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs, structure 3

Soczek, K.M., Doudna, J.A.

(2025) Nucleic Acids Res 53:

Released	2025-01-08
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Acidaminococcus sp. BV3L6 synthetic construct
Macromolecule	CRISPR-associated endonuclease Cas12a (protein) Non-target DNA strand (nucleic acid) Target DNA strand (nucleic acid) guide RNA (25-MER) (nucleic acid)

1 to 24 of 24 Structures

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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

1HUX | pdb_00001hux

1PIX | pdb_00001pix

1POI | pdb_00001poi

1XDW | pdb_00001xdw

4HYR | pdb_00004hyr

4KPU | pdb_00004kpu

4L1F | pdb_00004l1f

4L2I | pdb_00004l2i

5B43 | pdb_00005b43

5KK5 | pdb_00005kk5

5XH6 | pdb_00005xh6

5XH7 | pdb_00005xh7

8SFH | pdb_00008sfh

8SFI | pdb_00008sfi

8SFJ | pdb_00008sfj

8SFL | pdb_00008sfl

8SFN | pdb_00008sfn

8SFO | pdb_00008sfo

8SFP | pdb_00008sfp

8SFQ | pdb_00008sfq

8SFR | pdb_00008sfr

9CJH | pdb_00009cjh

9CJI | pdb_00009cji

9CJJ | pdb_00009cjj