RCSB PDB: Search

9B55 \| pdb_00009b55	Download File View File

Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 1

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.23 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	E3 ubiquitin-protein ligase pub2 (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV

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9B56 \| pdb_00009b56	Download File View File

Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 2

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.35 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	E3 ubiquitin-protein ligase pub2 (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV

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9B57 \| pdb_00009b57	Download File View File

Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 3

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.37 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	E3 ubiquitin-protein ligase pub2 (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV

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9B58 \| pdb_00009b58	Download File View File

Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 4

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.39 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	E3 ubiquitin-protein ligase pub2 (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV

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9B59 \| pdb_00009b59	Download File View File

Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 5

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.49 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	E3 ubiquitin-protein ligase pub2 (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV

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9B5A \| pdb_00009b5a	Download File View File

Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 6

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.65 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	E3 ubiquitin-protein ligase pub2 (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV

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9B5B \| pdb_00009b5b	Download File View File

Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 7

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.31 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	E3 ubiquitin-protein ligase pub2 (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV

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9B5C \| pdb_00009b5c	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - consensus map and model

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.5 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Large ribosomal subunit protein eL40B (protein) Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5D \| pdb_00009b5d	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 1 map and model from consensus

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Large ribosomal subunit protein eL40B (protein) Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5E \| pdb_00009b5e	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from consensus

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.81 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Large ribosomal subunit protein eL40B (protein) Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5F \| pdb_00009b5f	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 1 map and model (Ub(A)/ATP/Mg)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.78 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Polyubiquitin (protein) Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5G \| pdb_00009b5g	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 2 map and model (Ub(A)/ATP/Mg)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.67 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Large ribosomal subunit protein eL40B (protein) Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5H \| pdb_00009b5h	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 3 map and model (Ub(A)-AMP/PPi/Mg)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.69 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Large ribosomal subunit protein eL40B (protein) Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, AMP, MG, POP

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9B5I \| pdb_00009b5i	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 4 map and model (Ub(A)-AMP/PPi/Mg)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.7 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Polyubiquitin (protein) Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, AMP, MG, POP

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9B5J \| pdb_00009b5j	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 5 map and model (Ub(A)-AMP)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.86 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Large ribosomal subunit protein eL40B (protein) Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, AMP

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9B5K \| pdb_00009b5k	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 1 map and model from cluster 1 (Ub(A)/ATP/Mg)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.16 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Large ribosomal subunit protein eL40B (protein) Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5L \| pdb_00009b5l	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (Ub(A)-AMP)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Polyubiquitin (protein) Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, AMP

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9B5M \| pdb_00009b5m	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - consensus map and model

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.79 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5N \| pdb_00009b5n	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from consensus

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.12 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5O \| pdb_00009b5o	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from consensus

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.19 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5P \| pdb_00009b5p	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 1 map and model (ATP/Mg)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.08 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5Q \| pdb_00009b5q	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 2 map and model (ATP/Mg)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.95 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5R \| pdb_00009b5r	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 3 map and model (ATP/Mg)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.95 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5S \| pdb_00009b5s	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 4 map and model (ATP/Mg)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.96 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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9B5T \| pdb_00009b5t	Download File View File

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 5 map and model (ATP/Mg)

Kochanczyk, T., Lima, C.D.

(2024) Nature 633: 216-223

Released	2024-06-05
Method	ELECTRON MICROSCOPY 3.16 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein) Ubiquitin-conjugating enzyme E2 4 (protein)
Unique Ligands	A1AIV, ATP, MG

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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

9B55 | pdb_00009b55

9B56 | pdb_00009b56

9B57 | pdb_00009b57

9B58 | pdb_00009b58

9B59 | pdb_00009b59

9B5A | pdb_00009b5a

9B5B | pdb_00009b5b

9B5C | pdb_00009b5c

9B5D | pdb_00009b5d

9B5E | pdb_00009b5e

9B5F | pdb_00009b5f

9B5G | pdb_00009b5g

9B5H | pdb_00009b5h

9B5I | pdb_00009b5i

9B5J | pdb_00009b5j

9B5K | pdb_00009b5k

9B5L | pdb_00009b5l

9B5M | pdb_00009b5m

9B5N | pdb_00009b5n

9B5O | pdb_00009b5o

9B5P | pdb_00009b5p

9B5Q | pdb_00009b5q

9B5R | pdb_00009b5r

9B5S | pdb_00009b5s

9B5T | pdb_00009b5t