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X-RAY STRUCTURE OF THE C-TERMINAL ULP1 PROTEASE DOMAIN IN COMPLEX WITH SMT3, THE YEAST ORTHOLOG OF SUMO.
Descriptor:	UBITQUTIN-LIKE PROTEIN SMT3, ULP1 PROTEASE
Authors:	Mossessova, E, Lima, C.D.
Deposit date:	2000-04-17
Release date:	2000-06-07
Last modified:	2022-12-21
Method:	X-RAY DIFFRACTION (1.6 Å)
Cite:	Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol.Cell, 5, 2000

3EF1

The Structure of Fcp1, an essential RNA polymerase II CTD phosphatase
Descriptor:	MAGNESIUM ION, RNA polymerase II subunit A C-terminal domain phosphatase
Authors:	Ghosh, A, Lima, C.D.
Deposit date:	2008-09-07
Release date:	2008-12-02
Last modified:	2017-10-25
Method:	X-RAY DIFFRACTION (2.15 Å)
Cite:	The structure of Fcp1, an essential RNA polymerase II CTD phosphatase. Mol.Cell, 32, 2008

3EF0

The Structure of Fcp1, an essential RNA polymerase II CTD phosphatase
Descriptor:	MAGNESIUM ION, RNA polymerase II subunit A C-terminal domain phosphatase, TETRAFLUOROALUMINATE ION
Authors:	Ghosh, A, Lima, C.D.
Deposit date:	2008-09-07
Release date:	2008-12-02
Last modified:	2024-04-03
Method:	X-RAY DIFFRACTION (2.1 Å)
Cite:	The structure of Fcp1, an essential RNA polymerase II CTD phosphatase. Mol.Cell, 32, 2008

3RTX

Crystal structure of mammalian capping enzyme (Mce1) and Pol II CTD complex
Descriptor:	GUANINE, RNA Polymerase II C-terminal domain, mRNA-capping enzyme
Authors:	Ghosh, A, Lima, C.D.
Deposit date:	2011-05-04
Release date:	2011-06-29
Last modified:	2024-04-03
Method:	X-RAY DIFFRACTION (2.81 Å)
Cite:	Structural insights to how mammalian capping enzyme reads the CTD code. Mol.Cell, 43, 2011

3SAF

Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site
Descriptor:	Exosome component 10, MAGNESIUM ION, YTTRIUM (III) ION
Authors:	Januszyk, K, Liu, Q, Lima, C.D.
Deposit date:	2011-06-02
Release date:	2011-07-06
Last modified:	2023-09-13
Method:	X-RAY DIFFRACTION (2.5 Å)
Cite:	Activities of human RRP6 and structure of the human RRP6 catalytic domain. Rna, 17, 2011

3SAG

Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site
Descriptor:	Exosome component 10, MAGNESIUM ION, YTTRIUM (III) ION
Authors:	Januszyk, K, Liu, Q, Lima, C.D.
Deposit date:	2011-06-02
Release date:	2011-07-06
Last modified:	2023-09-13
Method:	X-RAY DIFFRACTION (2.7 Å)
Cite:	Activities of human RRP6 and structure of the human RRP6 catalytic domain. Rna, 17, 2011

3SAH

Crystal structure of the human RRP6 catalytic domain with Y436A mutation in the catalytic site
Descriptor:	Exosome component 10, MAGNESIUM ION, YTTRIUM (III) ION
Authors:	Januszyk, K, Liu, Q, Lima, C.D.
Deposit date:	2011-06-02
Release date:	2011-07-06
Last modified:	2023-09-13
Method:	X-RAY DIFFRACTION (2.65 Å)
Cite:	Activities of human RRP6 and structure of the human RRP6 catalytic domain. Rna, 17, 2011

3UIO

Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II
Descriptor:	E3 SUMO-protein ligase RanBP2, Ran GTPase-activating protein 1, SUMO-conjugating enzyme UBC9, ...
Authors:	Gareau, J.R, Reverter, D, Lima, C.D.
Deposit date:	2011-11-05
Release date:	2011-12-28
Last modified:	2023-09-13
Method:	X-RAY DIFFRACTION (2.602 Å)
Cite:	Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2. J.Biol.Chem., 287, 2012

3UIN

Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2
Descriptor:	E3 SUMO-protein ligase RanBP2, Ran GTPase-activating protein 1, SUMO-conjugating enzyme UBC9, ...
Authors:	Gareau, J.R, Reverter, D, Lima, C.D.
Deposit date:	2011-11-05
Release date:	2011-12-28
Last modified:	2023-09-13
Method:	X-RAY DIFFRACTION (2.597 Å)
Cite:	Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2. J.Biol.Chem., 287, 2012

3UIP

Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II
Descriptor:	E3 SUMO-protein ligase RanBP2, Ran GTPase-activating protein 1, SUMO-conjugating enzyme UBC9, ...
Authors:	Gareau, J.R, Reverter, D, Lima, C.D.
Deposit date:	2011-11-05
Release date:	2011-12-28
Last modified:	2023-09-13
Method:	X-RAY DIFFRACTION (2.293 Å)
Cite:	Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2. J.Biol.Chem., 287, 2012

3V62

Structure of the S. cerevisiae Srs2 C-terminal domain in complex with PCNA conjugated to SUMO on lysine 164
Descriptor:	ATP-dependent DNA helicase SRS2, N-ETHYLMALEIMIDE, Proliferating cell nuclear antigen, ...
Authors:	Armstrong, A.A, Mohideen, F, Lima, C.D.
Deposit date:	2011-12-18
Release date:	2012-02-29
Last modified:	2023-09-13
Method:	X-RAY DIFFRACTION (2.9 Å)
Cite:	Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2. Nature, 483, 2012

3V61

Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164
Descriptor:	BARIUM ION, N-ETHYLMALEIMIDE, Proliferating cell nuclear antigen, ...
Authors:	Armstrong, A.A, Mohideen, F, Lima, C.D.
Deposit date:	2011-12-18
Release date:	2012-02-29
Last modified:	2023-09-13
Method:	X-RAY DIFFRACTION (2.8 Å)
Cite:	Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2. Nature, 483, 2012

3V60

Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164
Descriptor:	Proliferating cell nuclear antigen, SULFATE ION, Ubiquitin-like protein SMT3
Authors:	Armstrong, A.A, Mohideen, F, Lima, C.D.
Deposit date:	2011-12-18
Release date:	2012-02-29
Last modified:	2023-09-13
Method:	X-RAY DIFFRACTION (2.6 Å)
Cite:	Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2. Nature, 483, 2012

4PZ7

PCE1 guanylyltransferase
Descriptor:	GLYCEROL, SULFATE ION, mRNA-capping enzyme subunit alpha
Authors:	Doamekpor, S.K, Lima, C.D.
Deposit date:	2014-03-28
Release date:	2014-06-25
Last modified:	2023-09-20
Method:	X-RAY DIFFRACTION (2.109 Å)
Cite:	How an mRNA capping enzyme reads distinct RNA polymerase II and Spt5 CTD phosphorylation codes. Genes Dev., 28, 2014

4PZ8

PCE1 guanylyltransferase bound to SPT5 CTD
Descriptor:	SULFATE ION, Transcription elongation factor spt5, mRNA-capping enzyme subunit alpha
Authors:	Doamekpor, S.K, Lima, C.D.
Deposit date:	2014-03-28
Release date:	2014-06-25
Last modified:	2023-09-20
Method:	X-RAY DIFFRACTION (3.1 Å)
Cite:	How an mRNA capping enzyme reads distinct RNA polymerase II and Spt5 CTD phosphorylation codes. Genes Dev., 28, 2014

4PZ6

PCE1 guanylyltransferase bound to SER2/SER5 phosphorylated RNA pol II CTD
Descriptor:	DNA-directed RNA polymerase II subunit rpb1, GUANOSINE, mRNA-capping enzyme subunit alpha
Authors:	Doamekpor, S.K, Lima, C.D.
Deposit date:	2014-03-28
Release date:	2014-06-25
Last modified:	2023-09-20
Method:	X-RAY DIFFRACTION (2.406 Å)
Cite:	How an mRNA capping enzyme reads distinct RNA polymerase II and Spt5 CTD phosphorylation codes. Genes Dev., 28, 2014

5D2M

Complex between human SUMO2-RANGAP1, UBC9 and ZNF451
Descriptor:	1,2-ETHANEDIOL, Ran GTPase-activating protein 1, SUMO-conjugating enzyme UBC9, ...
Authors:	Cappadocia, L, Lima, C.D.
Deposit date:	2015-08-05
Release date:	2015-11-04
Last modified:	2023-09-27
Method:	X-RAY DIFFRACTION (2.4 Å)
Cite:	Structural basis for catalytic activation by the human ZNF451 SUMO E3 ligase. Nat.Struct.Mol.Biol., 22, 2015

5FG1

Structure of the conserved yeast listerin (Ltn1) selenomethionine-substituted N-terminal domain, TRIGONAL FORM
Descriptor:	E3 ubiquitin-protein ligase listerin, POTASSIUM ION
Authors:	Doamekpor, S.K, Lima, C.D.
Deposit date:	2015-12-19
Release date:	2016-07-06
Last modified:	2019-11-20
Method:	X-RAY DIFFRACTION (2.55 Å)
Cite:	Structure and function of the yeast listerin (Ltn1) conserved N-terminal domain in binding to stalled 60S ribosomal subunits. Proc.Natl.Acad.Sci.USA, 113, 2016

8CT4

Cryo-EM structure of Mtb Lpd bound to inhibitor complex with 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide
Descriptor:	Dihydrolipoyl dehydrogenase, FLAVIN-ADENINE DINUCLEOTIDE, N~2~-(2-cyano-5-methyl-1H-indole-7-sulfonyl)-N~2~-methyl-N-[4-(oxetan-3-yl)-3,4-dihydro-2H-1,4-benzoxazin-7-yl]glycinamide
Authors:	Kochanczyk, T, Arango, N, Lima, C.D.
Deposit date:	2022-05-13
Release date:	2022-05-25
Last modified:	2023-06-07
Method:	ELECTRON MICROSCOPY (2.17 Å)
Cite:	Cryo-EM structure of Mtb Lpd bound to the inhibitor 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide at 2.17 Angstrom resolution Not published

8DAT

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB)
Descriptor:	ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, Cell division control protein 48, ...
Authors:	Lee, H.G, Lima, C.D.
Deposit date:	2022-06-14
Release date:	2022-11-30
Last modified:	2023-01-11
Method:	ELECTRON MICROSCOPY (3.8 Å)
Cite:	SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Proc.Natl.Acad.Sci.USA, 120, 2023

8DAU

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two folded ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA)
Descriptor:	ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, Cell division control protein 48, ...
Authors:	Lee, H.G, Lima, C.D.
Deposit date:	2022-06-14
Release date:	2022-11-30
Last modified:	2023-01-11
Method:	ELECTRON MICROSCOPY (3.7 Å)
Cite:	SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Proc.Natl.Acad.Sci.USA, 120, 2023

8DAV

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uC)
Descriptor:	ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, Cell division control protein 48, ...
Authors:	Lee, H.G, Lima, C.D.
Deposit date:	2022-06-14
Release date:	2022-11-30
Last modified:	2023-01-11
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Proc.Natl.Acad.Sci.USA, 120, 2023

8DAS

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intA)
Descriptor:	ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, Cell division control protein 48, ...
Authors:	Lee, H.G, Lima, C.D.
Deposit date:	2022-06-14
Release date:	2022-11-30
Last modified:	2023-01-11
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Proc.Natl.Acad.Sci.USA, 120, 2023

8DAW

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uD)
Descriptor:	ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, Cell division control protein 48, ...
Authors:	Lee, H.G, Lima, C.D.
Deposit date:	2022-06-14
Release date:	2022-11-30
Last modified:	2023-01-11
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Proc.Natl.Acad.Sci.USA, 120, 2023

8DAR

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP
Descriptor:	ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, Cell division control protein 48, ...
Authors:	Lee, H.G, Lima, C.D.
Deposit date:	2022-06-14
Release date:	2022-11-30
Last modified:	2023-01-11
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Proc.Natl.Acad.Sci.USA, 120, 2023

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Displayed results:	25
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