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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Cruz, V.E."

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Search Summary

This query matches 27 Structures.

Refinements

Structure Determination Methodology

experimental (27)

Scientific Name of Source Organism

	Saccharomyces cerevisiae BY4741 (18)
	Homo sapiens (6)
	Caenorhabditis elegans (2)
	Oryctolagus cuniculus (1)
	Saccharomyces cerevisiae (1)
	Saccharomyces cerevisiae BY4741-AV16 (1)

Taxonomy

Eukaryota (27)

Experimental Method

	ELECTRON MICROSCOPY (20)
	X-RAY DIFFRACTION (7)

Polymer Entity Type

	Protein (27)
	RNA (18)

Refinement Resolution (Å)

	1.5 - 2.0 (4)
	2.0 - 2.5 (5)
	2.5 - 3.0 (9)
	3.0 - 3.5 (7)
	3.5 - 4.0 (2)

Release Date

	2015 - 2019 (2)
	2020 - 2024 (25)

Enzyme Classification Name

	Transferases (15)
	Hydrolases (15)
	Lyases (1)

Symmetry Type

	Asymmetric (22)
	Cyclic (6)

AllSelected

1 to 25 of 27 Structures

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5JJ6 \| pdb_00005jj6	Download File View File

Fic-1 (aa134 - 508) from C. elegans

Cruz, V.E., Schwartz, T.U.

To be published

Released	2016-06-01
Method	X-RAY DIFFRACTION 2.907 Å
Organisms	Caenorhabditis elegans
Macromolecule	Adenosine monophosphate-protein transferase FICD homolog (protein)
Unique Ligands	SO4

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5JJ7 \| pdb_00005jj7	Download File View File

Fic-1 (aa134 - 508 E274G) from C. elegans

Cruz, V.E., Schwartz, T.U.

To be published

Released	2016-06-01
Method	X-RAY DIFFRACTION 3.749 Å
Organisms	Caenorhabditis elegans
Macromolecule	Adenosine monophosphate-protein transferase FICD homolog (protein)
Unique Ligands	SO4

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6WMD \| pdb_00006wmd	Download File View File

Human Sun2-KASH4 complex

Cruz, V.E., Schwartz, T.U.

(2020) J Mol Biology 432: 6028-6041

Released	2020-12-02
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	Nesprin-4 (protein) SUN domain-containing protein 2 (protein)
Unique Ligands	MG

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6WME \| pdb_00006wme	Download File View File

Human Sun2-KASH3 complex

Cruz, V.E., Schwartz, T.U.

(2020) J Mol Biology 432: 6028-6041

Released	2020-12-02
Method	X-RAY DIFFRACTION 1.53 Å
Organisms	Homo sapiens
Macromolecule	Nesprin-3 (protein) SUN domain-containing protein 2 (protein)
Unique Ligands	K

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6WMF \| pdb_00006wmf	Download File View File

Human Sun2-KASH5 complex

Cruz, V.E., Schwartz, T.U.

(2020) J Mol Biology 432: 6028-6041

Released	2020-12-02
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Protein KASH5 (protein) SUN domain-containing protein 2 (protein)
Unique Ligands	K

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6WMG \| pdb_00006wmg	Download File View File

Human Sun2 (500-717)

Cruz, V.E., Schwartz, T.U.

(2020) J Mol Biology 432: 6028-6041

Released	2020-12-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	SUN domain-containing protein 2 (protein)
Unique Ligands	K

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7NAC \| pdb_00007nac	Download File View File

State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.04 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 55 Unique nucleic acid chains: 3
Unique Ligands	SAH, ZN

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7NAD \| pdb_00007nad	Download File View File

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.04 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 24 Unique nucleic acid chains: 2
Unique Ligands	ZN

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7NAF \| pdb_00007naf	Download File View File

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.13 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 15 Unique nucleic acid chains: 1
Unique Ligands	SAH

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7R6K \| pdb_00007r6k	Download File View File

State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.17 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 15 Unique nucleic acid chains: 1

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7R6Q \| pdb_00007r6q	Download File View File

State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 2.98 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 16 Unique nucleic acid chains: 3

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7R72 \| pdb_00007r72	Download File View File

State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 local model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.07 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 22 Unique nucleic acid chains: 2
Unique Ligands	ZN

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7R7A \| pdb_00007r7a	Download File View File

State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.04 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 54 Unique nucleic acid chains: 3
Unique Ligands	ZN

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7R7C \| pdb_00007r7c	Download File View File

State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.71 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 10 Unique nucleic acid chains: 1

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7R7O \| pdb_00007r7o	Download File View File

Structure of methyltransferase domain of Spb1 boudn to SAM

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

To be published

Released	2022-06-29
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	AdoMet-dependent rRNA methyltransferase SPB1 (protein)
Unique Ligands	SAM

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7U0H \| pdb_00007u0h	Download File View File

State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-12-14
Method	ELECTRON MICROSCOPY 2.76 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 46 Unique nucleic acid chains: 3
Unique Ligands	MG, ZN

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7UOO \| pdb_00007uoo	Download File View File

Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state

Sekulski, K., Cruz, V.E., Weirich, C.S., Erzberger, J.P.

(2023) Nat Commun 14: 1207-1207

Released	2023-03-15
Method	ELECTRON MICROSCOPY 2.34 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 56 Unique nucleic acid chains: 4
Unique Ligands	B3P, GDP, GTP, K, MG, ZN

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7UQB \| pdb_00007uqb	Download File View File

Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4

Sekulski, K., Cruz, V.E., Weirich, C.S., Erzberger, J.P.

(2023) Nat Commun 14: 1207-1207

Released	2023-03-15
Method	ELECTRON MICROSCOPY 2.43 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 56 Unique nucleic acid chains: 4
Unique Ligands	ALF, B3P, GDP, K, MG, ZN

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7UQZ \| pdb_00007uqz	Download File View File

Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain

Sekulski, K., Cruz, V.E., Weirich, C.S., Erzberger, J.P.

(2023) Nat Commun 14: 1207-1207

Released	2023-03-15
Method	ELECTRON MICROSCOPY 2.44 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 56 Unique nucleic acid chains: 4
Unique Ligands	B3P, GDP, K, MG, ZN

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7UUI \| pdb_00007uui	Download File View File

Nucleoplasmic pre-60S intermediate of the Nog2 containing post-rotation state from a SPB1 D52A strain

Sekulski, K., Cruz, V.E., Weirich, C.S., Erzberger, J.P.

(2023) Nat Commun 14: 1207-1207

Released	2023-03-15
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Nucleolar GTP-binding protein 2 (protein)
Unique Ligands	GDP, K, MG

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7V08 \| pdb_00007v08	Download File View File

Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain

Sekulski, K., Cruz, V.E., Weirich, C.S., Erzberger, J.P.

(2023) Nat Commun 14: 1207-1207

Released	2023-03-15
Method	ELECTRON MICROSCOPY 2.36 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 56 Unique nucleic acid chains: 4
Unique Ligands	B3P, GDP, K, MG, ZN

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8V83 \| pdb_00008v83	Download File View File

60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)

Cruz, V.E., Weirich, C.S., Peddada, N., Erzberger, J.P.

(2024) Nat Commun 15: 3296-3296

Released	2024-05-01
Method	ELECTRON MICROSCOPY 2.53 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 45 Unique nucleic acid chains: 3
Unique Ligands	ZN

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8V84 \| pdb_00008v84	Download File View File

60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)

Cruz, V.E., Weirich, C.S., Peddada, N., Erzberger, J.P.

(2024) Nat Commun 15: 3296-3296

Released	2024-05-01
Method	ELECTRON MICROSCOPY 2.7 Å
Organisms	Saccharomyces cerevisiae BY4741 Saccharomyces cerevisiae BY4741-AV16
Macromolecule	Unique protein chains: 46 Unique nucleic acid chains: 3
Unique Ligands	GDP, MG, ZN

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8V85 \| pdb_00008v85	Download File View File

60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Low-pass filtered locally refined map)

Cruz, V.E., Weirich, C.S., Peddada, N., Erzberger, J.P.

(2024) Nat Commun 15: 3296-3296

Released	2024-05-01
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	ATP-dependent RNA helicase DBP10 (protein)

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8V87 \| pdb_00008v87	Download File View File

60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)

Cruz, V.E., Weirich, C.S., Peddada, N., Erzberger, J.P.

(2024) Nat Commun 15: 3296-3296

Released	2024-05-01
Method	ELECTRON MICROSCOPY 2.66 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 53 Unique nucleic acid chains: 3
Unique Ligands	ADP, GDP, K, MG, ZN

1 to 25 of 27 Structures

Page 1 of 2

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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

5JJ6 | pdb_00005jj6

5JJ7 | pdb_00005jj7

6WMD | pdb_00006wmd

6WME | pdb_00006wme

6WMF | pdb_00006wmf

6WMG | pdb_00006wmg

7NAC | pdb_00007nac

7NAD | pdb_00007nad

7NAF | pdb_00007naf

7R6K | pdb_00007r6k

7R6Q | pdb_00007r6q

7R72 | pdb_00007r72

7R7A | pdb_00007r7a

7R7C | pdb_00007r7c

7R7O | pdb_00007r7o

7U0H | pdb_00007u0h

7UOO | pdb_00007uoo

7UQB | pdb_00007uqb

7UQZ | pdb_00007uqz

7UUI | pdb_00007uui

7V08 | pdb_00007v08

8V83 | pdb_00008v83

8V84 | pdb_00008v84

8V85 | pdb_00008v85

8V87 | pdb_00008v87