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8DAR
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BU of 8dar by Molmil
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
8DAU
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BU of 8dau by Molmil
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
8DAW
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BU of 8daw by Molmil
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
8DAS
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BU of 8das by Molmil
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
8DAT
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BU of 8dat by Molmil
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
8DAV
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BU of 8dav by Molmil
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
4II2
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BU of 4ii2 by Molmil
Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4, ubiquitin, and ATP/Mg
Descriptor: 1,2-ETHANEDIOL, 2-(2-METHOXYETHOXY)ETHANOL, ADENOSINE-5'-TRIPHOSPHATE, ...
Authors:Olsen, S.K, Lima, C.D.
Deposit date:2012-12-19
Release date:2013-02-13
Last modified:2023-09-20
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer.
Mol.Cell, 49, 2013
4II3
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BU of 4ii3 by Molmil
Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1) in complex with ubiquitin and ATP/Mg
Descriptor: ADENOSINE-5'-TRIPHOSPHATE, CALCIUM ION, MAGNESIUM ION, ...
Authors:Olsen, S.K, Lima, C.D.
Deposit date:2012-12-19
Release date:2013-02-13
Last modified:2023-09-20
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer.
Mol.Cell, 49, 2013
7S7B
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BU of 7s7b by Molmil
Human Nuclear exosome targeting (NEXT) complex homodimer bound to RNA (substrate 1)
Descriptor: Exosome RNA helicase MTR4, RNA (46-MER), RNA-binding protein 7, ...
Authors:Puno, M.R, Lima, C.D.
Deposit date:2021-09-15
Release date:2022-06-15
Last modified:2022-06-22
Method:ELECTRON MICROSCOPY (4.06 Å)
Cite:Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex.
Cell, 185, 2022
7S7C
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BU of 7s7c by Molmil
Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2)
Descriptor: Exosome RNA helicase MTR4, RNA (30-MER), RNA-binding protein 7, ...
Authors:Puno, M.R, Lima, C.D.
Deposit date:2021-09-15
Release date:2022-06-15
Last modified:2022-06-22
Method:ELECTRON MICROSCOPY (3.62 Å)
Cite:Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex.
Cell, 185, 2022
4PZ7
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BU of 4pz7 by Molmil
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
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BU of 4pz8 by Molmil
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
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BU of 4pz6 by Molmil
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
1KNC
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BU of 1knc by Molmil
Structure of AhpD from Mycobacterium tuberculosis, a novel enzyme with thioredoxin-like activity.
Descriptor: AhpD protein, SULFATE ION
Authors:Bryk, R, Lima, C.D, Erdjument-Bromage, H, Tempst, P, Nathan, C.
Deposit date:2001-12-18
Release date:2002-01-23
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (2 Å)
Cite:Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein.
Science, 295, 2002
1KPS
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BU of 1kps by Molmil
Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1
Descriptor: Ran-GTPase activating protein 1, SULFATE ION, Ubiquitin-like protein SUMO-1 conjugating enzyme
Authors:Bernier-Villamor, V, Sampson, D.A, Matunis, M.J, Lima, C.D.
Deposit date:2002-01-02
Release date:2002-02-13
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1.
Cell(Cambridge,Mass.), 108, 2002
1LA2
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BU of 1la2 by Molmil
Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase
Descriptor: Myo-inositol-1-phosphate synthase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Authors:Kniewel, R, Buglino, J.A, Shen, V, Chadna, T, Beckwith, A, Lima, C.D, Burley, S.K, New York SGX Research Center for Structural Genomics (NYSGXRC)
Deposit date:2002-03-27
Release date:2002-04-10
Last modified:2021-02-03
Method:X-RAY DIFFRACTION (2.65 Å)
Cite:Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase
J.STRUCT.FUNCT.GENOM., 2, 2002
1LNZ
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BU of 1lnz by Molmil
Structure of the Obg GTP-binding protein
Descriptor: GUANOSINE-5',3'-TETRAPHOSPHATE, MAGNESIUM ION, SPO0B-associated GTP-binding protein
Authors:Buglino, J, Shen, V, Hakimian, P, Lima, C.D, Burley, S.K, New York SGX Research Center for Structural Genomics (NYSGXRC)
Deposit date:2002-05-04
Release date:2002-09-16
Last modified:2021-02-03
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural and biochemical analysis of the Obg GTP binding protein
Structure, 10, 2002
1LX7
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BU of 1lx7 by Molmil
Structure of E. coli uridine phosphorylase at 2.0A
Descriptor: uridine phosphorylase
Authors:Burling, T, Buglino, J.A, Kniewel, R, Chadna, T, Beckwith, A, Lima, C.D, Burley, S.K, New York SGX Research Center for Structural Genomics (NYSGXRC)
Deposit date:2002-06-04
Release date:2002-06-12
Last modified:2021-02-03
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structure of Escherichia coli uridine phosphorylase at 2.0 A.
Acta Crystallogr.,Sect.D, 59, 2003
1LY1
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BU of 1ly1 by Molmil
Structure and Mechanism of T4 Polynucleotide Kinase
Descriptor: SULFATE ION, polynucleotide kinase
Authors:Wang, L.K, Lima, C.D, Shuman, S.
Deposit date:2002-06-06
Release date:2002-07-17
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme.
EMBO J., 21, 2002
1NI5
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BU of 1ni5 by Molmil
Structure of the MesJ PP-ATPase from Escherichia Coli
Descriptor: Putative cell cycle protein mesJ
Authors:Gu, M, Burling, T, Lima, C.D, Burley, S.K, New York SGX Research Center for Structural Genomics (NYSGXRC)
Deposit date:2002-12-21
Release date:2003-01-07
Last modified:2021-02-03
Method:X-RAY DIFFRACTION (2.65 Å)
Cite:Structure of the MesJ PP-ATPase from Escherichia coli
To be Published
1NI3
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BU of 1ni3 by Molmil
Structure of the Schizosaccharomyces pombe YchF GTPase
Descriptor: SULFATE ION, YchF GTP-binding protein
Authors:Kniewel, R.K, Buglino, J.A, Lima, C.D, Burley, S.K, New York SGX Research Center for Structural Genomics (NYSGXRC)
Deposit date:2002-12-20
Release date:2003-01-07
Last modified:2021-02-03
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Structure of the S. pombe YchF GTP-binding protein
To be Published
1TQ8
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BU of 1tq8 by Molmil
Crystal Structure of protein Rv1636 from Mycobacterium tuberculosis H37Rv
Descriptor: hypothetical protein Rv1636
Authors:Rajashankar, K.R, Kniewel, R, Solorzano, V, Lima, C.D, Burley, S.K, New York SGX Research Center for Structural Genomics (NYSGXRC)
Deposit date:2004-06-16
Release date:2004-06-29
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal Structure of hypothetical protein Rv1636 from Mycobacterium tuberculosis H37Rv
To be Published
1XEA
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BU of 1xea by Molmil
Crystal structure of a Gfo/Idh/MocA family oxidoreductase from Vibrio cholerae
Descriptor: NICKEL (II) ION, Oxidoreductase, Gfo/Idh/MocA family
Authors:R Rajashankar, K, Reynes, J.A, Kniewel, R, Lima, C.D, Burley, S.K, New York SGX Research Center for Structural Genomics (NYSGXRC)
Deposit date:2004-09-09
Release date:2004-09-28
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (2.65 Å)
Cite:Crystal structure of a Gfo/Idh/MocA family oxidoreductase from Vibrio cholerae
To be Published
1XRH
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BU of 1xrh by Molmil
Crystal Structure of Ureidoglycolate Dehydrogenase from Escherichia Coli
Descriptor: Ureidoglycolate Dehydrogenase
Authors:Rajashankar, K.R, Kniewel, R, Lima, C.D, Burley, S.K, New York SGX Research Center for Structural Genomics (NYSGXRC)
Deposit date:2004-10-14
Release date:2004-10-26
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Crystal Structure of Ureidoglycolate Dehydrogenase from Escherichia Coli
To be Published
1XT9
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BU of 1xt9 by Molmil
Crystal Structure of Den1 in complex with Nedd8
Descriptor: Neddylin, Sentrin-specific protease 8
Authors:Reverter, D, Wu, K, Erdene, T.G, Pan, Z.Q, Wilkinson, K.D, Lima, C.D.
Deposit date:2004-10-21
Release date:2004-12-21
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structure of a Complex between Nedd8 and the Ulp/Senp Protease Family Member Den1.
J.Mol.Biol., 345, 2005

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