Electron Microscopy Data Bank

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Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer

Release date: April 17, 2024
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8q7h
Q-score: 0.39

Horn-Ghetko D, Hopf LVM, Tripathi-Giesgen I, Du J, Kostrhon S, Vu DT, Beier V, Steigenberger B, Prabu JR, Stier L, Bruss EM, Mann M, Xiong Y, Schulman BA

Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01257-y Pubmed: 38605244 ]

Sample:

E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
Structure of cul9-rbx1 ubiquitin e3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer (Complex from Homo sapiens)
Unknown (12 kDa, Protein from Homo sapiens)
Cullin-9 (281 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Nedd8 (9 kDa, Protein from Homo sapiens)

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EMD-19856

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Focused map 1- K48-linked ubiquitin chain formation with a cullin-RING E3 ligase Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

Release date: April 10, 2024
Resolution: 3.55 Å
EM Method: Single-particle

Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G

Nat Struct Mol Biol (2024) 31 pp. 378-389 [ DOI: doi:10.1038/s41594-023-01206-1 Pubmed: 38326650 ]

Sample:

E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
Cullin-2 (87 kDa, Protein from Homo sapiens)
Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
Elongin-b (elob), elongin-c (eloc), protein fem-1 homolog c (fem1c) and trapped ube2r2-donor ub-acceptor ub-sil1 peptide (Complex from Homo sapiens)
K48-linked ubiquitin chain formation with a cullin-ring e3 ligase and cdc34:nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2-donor ub-acceptor ub-sil1 peptide (190 kDa, Complex)
Elongin-c (12 kDa, Protein from Homo sapiens)
Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
Elongin-b (13 kDa, Protein from Homo sapiens)
Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)

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EMD-19857

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Focused map 2 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

Release date: April 10, 2024
Resolution: 3.76 Å
EM Method: Single-particle

Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G

Nat Struct Mol Biol (2024) 31 pp. 378-389 [ DOI: doi:10.1038/s41594-023-01206-1 Pubmed: 38326650 ]

Sample:

Cdc34, nedd8, fem1c with ube2r2-donor ub-acceptor ub-sil1 peptide and k48-linked ubiquitin chain (Complex from Homo sapiens)
Ubiquitin (77 kDa, Protein from Homo sapiens)
K48-linked ubiquitin chain formation with a cullin-ring e3 ligase and cdc34:nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2-donor ub-acceptor ub-sil1 peptide (190 kDa, Complex)
Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
Ring e3 ligase (rbx1) (Complex from Homo sapiens)
Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)

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EMD-19858

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Focused map 3 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

Release date: April 10, 2024
Resolution: 3.89 Å
EM Method: Single-particle

Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G

Nat Struct Mol Biol (2024) 31 pp. 378-389 [ DOI: doi:10.1038/s41594-023-01206-1 Pubmed: 38326650 ]

Sample:

E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
K48-linked ubiquitin chain formation with a cullin-ring e3 ligase and cdc34:nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2-donor ub-acceptor ub-sil1 peptide (190 kDa, Complex)
Cdc34, nedd8, fem1c with ube2r2-donor ub-acceptor ub-sil1 peptide and k48-linked ubiquitin chain (Complex from 9606)
Ubiquitin (77 kDa, Protein from Homo sapiens)
Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
Ring e3 ligase (rbx1) (Complex from Homo sapiens)

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EMD-19859

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Focused map 4 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

Release date: April 10, 2024
Resolution: 3.89 Å
EM Method: Single-particle

Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G

Nat Struct Mol Biol (2024) 31 pp. 378-389 [ DOI: doi:10.1038/s41594-023-01206-1 Pubmed: 38326650 ]

Sample:

E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
Cullin-2 (87 kDa, Protein from Homo sapiens)
Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
K48-linked ubiquitin chain formation with a cullin-ring e3 ligase and cdc34:nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2-donor ub-acceptor ub-sil1 peptide (190 kDa, Complex)
Ubiquitin (77 kDa, Protein from Homo sapiens)
Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
Cdc34, nedd8, fem1c with ube2r2-donor ub-acceptor ub-sil1 peptide and k48-linked ubiquitin chain (Complex from Homo sapiens)

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EMD-19860

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Focused map 5 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

Release date: April 10, 2024
Resolution: 3.94 Å
EM Method: Single-particle

Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G

Nat Struct Mol Biol (2024) 31 pp. 378-389 [ DOI: doi:10.1038/s41594-023-01206-1 Pubmed: 38326650 ]

Sample:

Cdc34, nedd8, fem1c with ube2r2-donor ub-acceptor ub-sil1 peptide and k48-linked ubiquitin chain (Complex from Homo sapiens)
Ubiquitin (77 kDa, Protein from Homo sapiens)
Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
K48-linked ubiquitin chain formation with a cullin-ring e3 ligase and cdc34:nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2-donor ub-acceptor ub-sil1 peptide (190 kDa, Complex)
Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
Cullin-2 (87 kDa, Protein from Homo sapiens)
Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)

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EMD-17800

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NEDD8-CUL2-RBX1-ELOB/C-FEM1C-SIL1 conformation 1

Release date: Feb. 14, 2024
Resolution: 7.19 Å
EM Method: Single-particle

Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G

Nat Struct Mol Biol (2024) 31 pp. 378-389 [ DOI: doi:10.1038/s41594-023-01206-1 Pubmed: 38326650 ]

Sample:

Nedd8-cul2-rbx1-elob/c-fem1c-sil1 conformation 1 (200 kDa, Complex from Homo sapiens)

EMD-17801

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NEDD8-CUL2-RBX1-ELOB/C-FEM1C-SIL1 conformation 2

Release date: Feb. 14, 2024
Resolution: 6.88 Å
EM Method: Single-particle

Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G

Nat Struct Mol Biol (2024) 31 pp. 378-389 [ DOI: doi:10.1038/s41594-023-01206-1 Pubmed: 38326650 ]

Sample:

Nedd8-cul2-rbx1-elob/c-fem1c-sil1 conformation 2 (200 kDa, Complex from Homo sapiens)

EMD-17802

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K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL1-RBX1-SKP1-FBXW7 with trapped UBE2R2-donor UB-acceptor UB-cyclin E peptide

Release date: Feb. 14, 2024
Resolution: 8.12 Å
EM Method: Single-particle

Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G

Nat Struct Mol Biol (2024) 31 pp. 378-389 [ DOI: doi:10.1038/s41594-023-01206-1 Pubmed: 38326650 ]

Sample:

K48-linked ubiquitin chain formation with a cullin-ring e3 ligase & cdc34: nedd8-cul1-rbx1-skp1-fbxw7 with trapped ube2r2~donor ub~acceptor ub-cyclin e peptide (220 kDa, Complex from Homo sapiens)

EMD-17803

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Consensus map - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide

Release date: Feb. 14, 2024
Resolution: 3.76 Å
EM Method: Single-particle

Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G

Nat Struct Mol Biol (2024) 31 pp. 378-389 [ DOI: doi:10.1038/s41594-023-01206-1 Pubmed: 38326650 ]

Sample:

Consensus map - k48-linked ubiquitin chain formation with a cullin-ring e3 ligase & cdc34: nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2~donor ub~acceptor ub-sil1 peptide (190 kDa, Complex from Homo sapiens)

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