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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "RBCK1"

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Search Summary

This query matches 13 Structures.

Refinements

Structure Determination Methodology

experimental (13)

Scientific Name of Source Organism

	Homo sapiens (11)
	Mus musculus (4)

Taxonomy

Eukaryota (13)

Experimental Method

	X-RAY DIFFRACTION (11)
	SOLUTION NMR (2)

Polymer Entity Type

Protein (13)

Refinement Resolution (Å)

	1.5 - 2.0 (5)
	2.0 - 2.5 (3)
	2.5 - 3.0 (2)
	3.0 - 3.5 (1)

Release Date

	2010 - 2014 (4)
	2015 - 2019 (1)
	2020 - 2024 (8)

Enzyme Classification Name

	Transferases (13)
	Ligases (2)

Symmetry Type

	Asymmetric (11)
	Cyclic (2)

SCOP Classification

Alpha and beta proteins (a+b) (2)

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1 to 13 of 13 Structures

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2LGY \| pdb_00002lgy	Download File View File

Ubiquitin-like domain from HOIL-1

Beasley, S.A., Shaw, G.S.

(2012) Protein Sci 21: 1085-1092

Released	2012-06-20
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)

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3B08 \| pdb_00003b08	Download File View File

Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin

Sato, Y., Fujita, H., Yoshikawa, A., Yamashita, M., Yamagata, A., Kaiser, S.E., Iwai, K., Fukai, S.

(2011) Proc Natl Acad Sci U S A 108: 20520-20525

Released	2011-12-14
Method	X-RAY DIFFRACTION 1.701 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Polyubiquitin-C (protein) RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)
Unique Ligands	ZN
Unique branched monosaccharides	GLC

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3B0A \| pdb_00003b0a	Download File View File

Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin

Sato, Y., Fujita, H., Yoshikawa, A., Yamashita, M., Yamagata, A., Kaiser, S.E., Iwai, K., Fukai, S.

(2011) Proc Natl Acad Sci U S A 108: 20520-20525

Released	2011-12-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Polyubiquitin-C (protein) RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)
Unique Ligands	TAM, ZN

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4DBG \| pdb_00004dbg	Download File View File

Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative

Yagi, H., Hiromoto, T., Mizushima, T., Kurimoto, E., Kato, K.

(2012) EMBO Rep 13: 462-468

Released	2012-04-04
Method	X-RAY DIFFRACTION 2.71 Å
Organisms	Homo sapiens
Macromolecule	RING finger protein 31 (protein) RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)

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5Y3T \| pdb_00005y3t	Download File View File

Crystal structure of hetero-trimeric core of LUBAC: HOIP double-UBA complexed with HOIL-1L UBL and SHARPIN UBL

Tokunaga, A., Fujita, H., Ariyoshi, M., Ohki, I., Tochio, H., Iwai, K., Shirakawa, M.

(2018) Cell Rep 23: 1192-1204

Released	2018-05-02
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus
Macromolecule	E3 ubiquitin-protein ligase RNF31 (protein) RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein) Sharpin (protein)
Unique Ligands	GOL

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7YUI \| pdb_00007yui	Download File View File

Crystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin

Xiao, L., Pan, L.

(2023) Sci Adv 9: eadi4599-eadi4599

Released	2023-08-30
Method	X-RAY DIFFRACTION 2.599 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-C (protein) RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)
Unique Ligands	ZN

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7YUJ \| pdb_00007yuj	Download File View File

Crystal structure of HOIL-1L(365-510)

Xiao, L., Pan, L.

(2023) Sci Adv 9: eadi4599-eadi4599

Released	2023-08-30
Method	X-RAY DIFFRACTION 1.865 Å
Organisms	Homo sapiens
Macromolecule	RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)
Unique Ligands	PEG, ZN

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8BVL \| pdb_00008bvl	Download File View File

Crystal structure of the IBR-RING2 domain of HOIL-1

Stieglitz, B., Koliopoulos, M.G., Rittinger, K.

(2022) Front Mol Biosci 9: 1098144-1098144

Released	2023-01-18
Method	X-RAY DIFFRACTION 2.24 Å
Organisms	Homo sapiens
Macromolecule	RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)
Unique Ligands	ZN

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8EAZ \| pdb_00008eaz	Download File View File

HOIL-1/E2-Ub/Ub transthiolation complex

Wang, X.S., Cotton, T.R., Lechtenberg, B.C.

(2023) Nat Commun 14: 168-168

Released	2023-01-18
Method	X-RAY DIFFRACTION 3.08 Å
Organisms	Homo sapiens
Macromolecule	RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 L3 (protein)
Unique Ligands	ZN

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8IM5 \| pdb_00008im5	Download File View File

Solution structure of the mouse HOIL1-L NZF domain in the free form

Walinda, E., Morimoto, D.

(2023) J Biological Chem 299: 105165-105165

Released	2023-08-30
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)
Unique Ligands	ZN

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8K6Q \| pdb_00008k6q	Download File View File

Crystal structure of HOIL-1L LTM domain

Yan, Z., Pan, L.F.

(2023) Biochem Biophys Res Commun 689: 149239-149239

Released	2024-07-03
Method	X-RAY DIFFRACTION 1.59 Å
Organisms	Homo sapiens
Macromolecule	RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)

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9EGV \| pdb_00009egv	Download File View File

HOIL-1 RING2 domain bound to ubiquitin

Wang, X.S., Lechtenberg, B.C.

(2024) bioRxiv

Released	2024-12-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-C (protein) RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)
Unique Ligands	CL, SO4, ZN

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9EGW \| pdb_00009egw	Download File View File

HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled)

Wang, X.S., Lechtenberg, B.C.

(2024) bioRxiv

Released	2024-12-11
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-C (protein) RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)
Unique Ligands	CL, SO4, ZN

1 to 13 of 13 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

2LGY | pdb_00002lgy

Ubiquitin-like domain from HOIL-1

3B08 | pdb_00003b08

Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin

3B0A | pdb_00003b0a

Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin

4DBG | pdb_00004dbg

Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative

5Y3T | pdb_00005y3t

Crystal structure of hetero-trimeric core of LUBAC: HOIP double-UBA complexed with HOIL-1L UBL and SHARPIN UBL

7YUI | pdb_00007yui

Crystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin

7YUJ | pdb_00007yuj

Crystal structure of HOIL-1L(365-510)

8BVL | pdb_00008bvl

Crystal structure of the IBR-RING2 domain of HOIL-1

8EAZ | pdb_00008eaz

HOIL-1/E2-Ub/Ub transthiolation complex

8IM5 | pdb_00008im5

Solution structure of the mouse HOIL1-L NZF domain in the free form

8K6Q | pdb_00008k6q

Crystal structure of HOIL-1L LTM domain

9EGV | pdb_00009egv

HOIL-1 RING2 domain bound to ubiquitin

9EGW | pdb_00009egw

HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled)

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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

2LGY | pdb_00002lgy

3B08 | pdb_00003b08

3B0A | pdb_00003b0a

4DBG | pdb_00004dbg

5Y3T | pdb_00005y3t

7YUI | pdb_00007yui

7YUJ | pdb_00007yuj

8BVL | pdb_00008bvl

8EAZ | pdb_00008eaz

8IM5 | pdb_00008im5

8K6Q | pdb_00008k6q

9EGV | pdb_00009egv

9EGW | pdb_00009egw