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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ordureau, A."

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Search Summary

This query matches 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	Homo sapiens (14)
	Saccharomyces cerevisiae S288C (6)
	Saccharomyces cerevisiae (3)
	Homo sapiens environmental sample (1)
	Rattus norvegicus (1)

Taxonomy

Eukaryota (20)

Experimental Method

	ELECTRON MICROSCOPY (13)
	X-RAY DIFFRACTION (7)

Polymer Entity Type

	Protein (20)
	RNA (6)

Refinement Resolution (Å)

	2.0 - 2.5 (4)
	2.5 - 3.0 (3)
	3.0 - 3.5 (9)
	3.5 - 4.0 (2)
	> 4.5 (2)

Release Date

	2015 - 2019 (9)
	2020 - 2024 (11)

Enzyme Classification Name

	Transferases (12)
	Translocases (5)
	Ligases (4)
	Lyases (1)

Membrane Protein Annotation

	MemProtMD (5)
	OPM (5)
	PDBTM (5)
	mpstruc (4)

Symmetry Type

Asymmetric (20)

SCOP Classification

	Alpha and beta proteins (a+b) (7)
	Artifacts (4)
	All beta proteins (2)

AllSelected

1 to 20 of 20 Structures

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5C7J	Download File View File

CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT

Walker, J.R., Hu, J., Dong, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Tong, Y., Structural Genomics Consortium (SGC)

(2016) Mol Cell 62: 121-136

Released	2016-03-16
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase NEDD4 (protein) Polyubiquitin-C (protein)

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5C7M	Download File View File

CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT

Walker, J.R., Hu, J., Dong, A., Wernimont, A., Zhang, W., Sidhu, S., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Tong, Y., Structural Genomics Consortium (SGC)

(2016) Mol Cell 62: 121-136

Released	2016-03-16
Method	X-RAY DIFFRACTION 3.03 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase Itchy homolog (protein) Polyubiquitin-C (protein)

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5HPK	Download File View File

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: NEDD4L and UbV NL.1

Wu, K.-P., Mukherjee, M., Mercredi, P.Y., Schulman, B.A.

(2016) Mol Cell 62: 121-136

Released	2016-03-16
Method	X-RAY DIFFRACTION 2.431 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase NEDD4-like (protein) Ubiquitin variant NL.1 (protein)

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5HPL	Download File View File

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: Rsp5 and UbV R5.4

Wu, K.-P., Kamadurai, H.B., Schulman, B.A.

(2016) Mol Cell 62: 121-136

Released	2016-03-16
Method	X-RAY DIFFRACTION 2.31 Å
Organisms	Homo sapiens Saccharomyces cerevisiae
Macromolecule	Rsp5 (protein) Ubiquitin variant R5.4 (protein)

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5HPS	Download File View File

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1 and UbV P1.1

Wu, K.-P., Mercredi, P.Y., Schulman, B.A.

(2016) Mol Cell 62: 121-136

Released	2016-03-16
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin variant P1.1 (protein) WWP1 HECT (protein)

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5HPT	Download File View File

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1, Ubv P2.3 and UBCH7

Wu, K.-P., Schulman, B.A.

(2016) Mol Cell 62: 121-136

Released	2016-03-16
Method	X-RAY DIFFRACTION 2.84 Å
Organisms	Homo sapiens
Macromolecule	NEDD4-like E3 ubiquitin-protein ligase WWP1 (protein) Ubiquitin variant P2.3 (protein) Ubiquitin-conjugating enzyme E2 L3 (protein)

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5JG6	Download File View File

APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C

Brown, N.G., Zhang, W., Yu, S., Miller, D.J., Sidhu, S.S., Schulman, B.A.

(2016) Cell 165: 1440-1453

Released	2016-06-15
Method	X-RAY DIFFRACTION 2.0013 Å
Organisms	Homo sapiens
Macromolecule	Anaphase-promoting complex subunit 11 (protein) Polyubiquitin-B (protein)
Unique Ligands	ZN

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5L9T	Download File View File

Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination where UBE2S, APC2, and APC11 are modeled into low resolution density

Brown, N.G., VanderLinden, R., Dube, P., Haselbach, D., Peters, J.M., Stark, H., Schulman, B.A.

(2016) Cell 165: 1440-1453

Released	2016-10-26
Method	ELECTRON MICROSCOPY 6.4 Å
Organisms	Homo sapiens Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 17

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5L9U	Download File View File

Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with a cross linked Ubiquitin variant-substrate-UBE2C (UBCH10) complex representing key features of multiubiquitination

Brown, N.G., VanderLinden, R., Dube, P., Haselbach, D., Peters, J.M., Stark, H., Schulman, B.A.

(2016) Cell 165: 1440-1453

Released	2016-09-14
Method	ELECTRON MICROSCOPY 6.4 Å
Organisms	Homo sapiens Rattus norvegicus Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 17

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6XMP	Download File View File

Structure of P5A-ATPase Spf1, Apo form

Park, E., Sim, S.I.

(2020) Science 369:

Released	2020-09-23
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	P5A-type ATPase (protein)
Unique Ligands	LMT

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6XMQ	Download File View File

Structure of P5A-ATPase Spf1, AMP-PCP-bound form

Park, E., Sim, S.I.

(2020) Science 369:

Released	2020-09-23
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	P5A-type ATPase (protein)
Unique Ligands	ACP, MG

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6XMS	Download File View File

Structure of P5A-ATPase Spf1, AlF4-bound form

Park, E., Sim, S.I.

(2020) Science 369:

Released	2020-09-23
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	P5A-type ATPase (protein)
Unique Ligands	ALF, MG

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6XMT	Download File View File

Structure of P5A-ATPase Spf1, BeF3-bound form

Park, E., Sim, S.I.

(2020) Science 369:

Released	2020-09-23
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	P5A-type ATPase (protein)
Unique Ligands	BEF, MG

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6XMU	Download File View File

Structure of P5A-ATPase Spf1, endogenous substrate-bound

Park, E., Sim, S.I.

(2020) Science 369:

Released	2020-09-23
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	P5A-type ATPase (protein) Putative endogenous substrate transmembrane helix (protein)
Unique Ligands	BEF, MG

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6ZVH	Download File View File

EDF1-ribosome complex

Best, K.M., Denk, T., Cheng, J., Thoms, M., Berninghausen, O., Beckmann, R.

(2020) Elife 9:

Released	2020-08-19
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 35 Unique nucleic acid chains: 2
Unique Ligands	MG, ZN

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6ZVI	Download File View File

Mbf1-ribosome complex

Best, K.M., Denk, T., Cheng, J., Thoms, M., Berninghausen, O., Beckmann, R.

(2020) Elife 9:

Released	2020-09-09
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 34 Unique nucleic acid chains: 4
Unique Ligands	ZN

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8OHD	Download File View File

60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native)

Penchev, I., DaRosa, P.A., Becker, T., Beckmann, R., Kopito, R.

(2024) Nature 627: 445-452

Released	2024-02-21
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 47 Unique nucleic acid chains: 3
Unique Ligands	MG, ZN

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8OJ0	Download File View File

60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native)

Penchev, I., DaRosa, P.A., Becker, T., Beckmann, R., Kopito, R.

(2024) Nature 627: 445-452

Released	2024-02-21
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens Homo sapiens environmental sample
Macromolecule	Unique protein chains: 50 Unique nucleic acid chains: 3
Unique Ligands	MG, ZN

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8OJ5	Download File View File

60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution)

Penchev, I., DaRosa, P.A., Peter, J.J., Kulathu, Y., Becker, T., Beckmann, R., Kopito, R.

(2024) Nature 627: 445-452

Released	2024-02-21
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 46 Unique nucleic acid chains: 3
Unique Ligands	MG, ZN

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8OJ8	Download File View File

60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native)

Penchev, I., DaRosa, P.A., Becker, T., Beckmann, R., Kopito, R.

(2024) Nature 627: 445-452

Released	2024-02-21
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 47 Unique nucleic acid chains: 3
Unique Ligands	MG, ZN