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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "UBE2D3"

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Search Summary

This query matches 43 Structures.

Refinements

Structure Determination Methodology

experimental (43)

Scientific Name of Source Organism

	Homo sapiens (43)
	synthetic construct (2)
	Legionella pneumophila (1)
	Rattus norvegicus (1)
	Xenopus laevis (1)
	Xenopus tropicalis (1)

Taxonomy

	Eukaryota (43)
	other sequences (2)
	Bacteria (1)

Experimental Method

	ELECTRON MICROSCOPY (24)
	X-RAY DIFFRACTION (18)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (43)
	DNA (25)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (8)
	2.5 - 3.0 (3)
	3.0 - 3.5 (14)
	3.5 - 4.0 (13)
	4.0 - 4.5 (2)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (4)
	2015 - 2019 (4)
	2020 - 2024 (34)

Enzyme Classification Name

	Transferases (43)
	Ligases (7)

Symmetry Type

	Asymmetric (42)
	Cyclic (2)

SCOP Classification

	Alpha and beta proteins (a+b) (9)
	Artifacts (7)
	Small proteins (1)

AllSelected

1 to 25 of 43 Structures

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2FUH	Download File View File

Solution Structure of the UbcH5c/Ub Non-covalent Complex

Brzovic, P.S., Lissounov, A., Hoyt, D.W., Klevit, R.E.

(2006) Mol Cell 21: 873-880

Released	2006-03-28
Method	SOLUTION NMR
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 D3 (protein)

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3L1Z	Download File View File

Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme

Benirschke, R., Thompson, J.R., Mer, G.

(2010) Structure 18: 955-965

Released	2010-05-05
Method	X-RAY DIFFRACTION 3.17 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin conjugation factor E4 B (protein) Ubiquitin-conjugating enzyme E2 D3 (protein)

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3RPG	Download File View File

Bmi1/Ring1b-UbcH5c complex structure

Bentley, M.L., Dong, K.C., Cochran, A.G.

(2011) EMBO J 30: 3285-3297

Released	2011-08-17
Method	X-RAY DIFFRACTION 2.6485 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RING2 (protein) Polycomb complex protein BMI-1 (protein) Ubiquitin-conjugating enzyme E2 D3 (protein)
Unique Ligands	ZN

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3UGB	Download File View File

UbcH5c~Ubiquitin Conjugate

Page, R.C., Pruneda, J.N., Klevit, R.E., Misra, S.

(2012) Biochemistry 51: 4175-4187

Released	2012-05-16
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-C (protein) Ubiquitin-conjugating enzyme E2 D3 (protein)
Unique Ligands	GOL

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4R8P	Download File View File

Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle

McGinty, R.K., Henrici, R.C., Tan, S.

(2014) Nature 514: 591-596

Released	2014-11-05
Method	X-RAY DIFFRACTION 3.2846 Å
Organisms	Homo sapiens Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ZN

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4S3O	Download File View File

PCGF5-RING1B-UbcH5c complex

Taherbhoy, A.M., Cochran, A.G.

(2015) Nat Commun 6: 7621-7621

Released	2015-07-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RING2 (protein) Polycomb group RING finger protein 5 (protein) Ubiquitin-conjugating enzyme E2 D3 (protein)
Unique Ligands	ZN

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5EGG	Download File View File

Crystal structure of human ubiquitin-conjugating enzyme UBCH5C

Zhu, L., Li, H., Wu, F., Zhu, J.

(2017) Acta Pharm Sin B 7: 390-394

Released	2016-11-02
Method	X-RAY DIFFRACTION 1.76 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 D3 (protein)

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5IFR	Download File View File

Structure of the stable UBE2D3-UbDha conjugate

Pruneda, J.N., Mulder, M.P.C., Witting, K., Ovaa, H., Komander, D.

(2016) Nat Chem Biol 12: 523-530

Released	2016-05-11
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-B (protein) Ubiquitin-conjugating enzyme E2 D3 (protein)
Unique Ligands	GOL

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6CP0	Download File View File

SdcA in complex with the E2, UbcH5C

Wasilko, D.J., Huang, Q., Mao, Y.

(2018) Elife 7:

Released	2018-08-01
Method	X-RAY DIFFRACTION 3.01 Å
Organisms	Homo sapiens Legionella pneumophila
Macromolecule	SdcA (protein) Ubiquitin-conjugating enzyme E2 D3 (protein)

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6T7F	Download File View File

RCR E3 ligase E2-Ubiquitin transthiolation intermediate

Mabbitt, P.D., Virdee, S.

(2020) Nat Chem Biol 16: 1227-1236

Released	2020-08-05
Method	X-RAY DIFFRACTION 2.58 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase MYCBP2 (protein) Polyubiquitin-C (protein) Ubiquitin-conjugating enzyme E2 D3 (protein)
Unique Ligands	LWZ, ZN

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7AHZ	Download File View File

Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub

Magnussen, H.M., Huang, D.T.

(2021) J Mol Biol 433: 166807-166807

Released	2021-01-20
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Homo sapiens Xenopus tropicalis
Macromolecule	E3 ubiquitin-protein ligase Mdm2 (protein) Polyubiquitin-B (protein) Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast) (protein)
Unique Ligands	CL, ZN

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7JZV	Download File View File

Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome

Witus, S.R., Burrell, A.L., Hansen, J.M., Farrell, D.P., Dimaio, F., Kollman, J.M., Klevit, R.E.

(2021) Nat Struct Mol Biol 28: 268-277

Released	2021-02-17
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ZN

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7LYB	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c

Hu, Q., Botuyan, M.V., Zhao, D., Cui, D., Mer, E., Mer, G.

(2021) Nature 596: 438-443

Released	2021-07-28
Method	ELECTRON MICROSCOPY 3.28 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8AMS	Download File View File

Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin

Perez-Borrajero, C., Kotova, I., Murciano, B., Hennig, J.

To be published

Released	2023-11-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-C (protein) Tripartite motif-containing protein 2 (protein) Ubiquitin-conjugating enzyme E2 D3 (protein)
Unique Ligands	GOL, PE8, ZN

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8GRQ	Download File View File

Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome

Ai, H.S., Zebin, T., Zhiheng, D., Jiakun, T., Liying, Z., Jia-Bin, L., Man, P., Liu, L.

(2023) Chem

Released	2023-04-12
Method	ELECTRON MICROSCOPY 3.87 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8SMW	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1)

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, G.

(2024) Mol Cell 84: 839-853.e12

Released	2024-01-17
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8SMX	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2)

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, G.

(2024) Mol Cell 84: 839-853.e12

Released	2024-01-17
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8SMY	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3)

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, G.

(2024) Mol Cell 84: 839-853.e12

Released	2024-01-17
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8SMZ	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4)

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, G.

(2024) Mol Cell 84: 839-853.e12

Released	2024-01-17
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8SN0	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5)

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, G.

(2024) Mol Cell 84: 839-853.e12

Released	2024-01-17
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8SN1	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6)

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, G.

(2024) Mol Cell 84: 839-853.e12

Released	2024-01-17
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8SN2	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A)

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, G.

(2024) Mol Cell 84: 839-853.e12

Released	2024-01-17
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8SN3	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1)

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, G.

(2024) Mol Cell 84: 839-853.e12

Released	2024-01-17
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2
Unique Ligands	ZN

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8SN4	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2)

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, G.

(2024) Mol Cell 84: 839-853.e12

Released	2024-01-17
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2
Unique Ligands	ZN

Explore in 3D

8SN5	Download File View File

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3)

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, G.

(2024) Mol Cell 84: 839-853.e12

Released	2024-01-17
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2
Unique Ligands	ZN

1 to 25 of 43 Structures

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