PDB Search results for query - Protein Data Bank Japan

PDB: 434 results

B. halodurans RNase H catalytic domain E188A mutant in complex with Mg2+ and RNA/DNA hybrid (reaction product)
Descriptor:	5'-D(APTPGPTPCPG)-3', 5'-R(PUPCPGPAPCPA)-3', ETHANOL, ...
Authors:	Nowotny, M, Yang, W.
Deposit date:	2006-03-03
Release date:	2006-04-25
Last modified:	2023-08-30
Method:	X-RAY DIFFRACTION (1.85 Å)
Cite:	Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. Embo J., 25, 2006

2G6O

Structure of bovine eNOS heme domain (BH4-free) complexed with CO
Descriptor:	ACETATE ION, ARGININE, CACODYLATE ION, ...
Authors:	Li, H, Igarashi, J, Jamal, J, Yang, W, Poulos, T.L.
Deposit date:	2006-02-24
Release date:	2006-08-08
Last modified:	2024-02-14
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	Structural studies of constitutive nitric oxide synthases with diatomic ligands bound. J.Biol.Inorg.Chem., 11, 2006

2G6H

Structure of rat nNOS heme domain (BH4 bound) in the reduced form
Descriptor:	5,6,7,8-TETRAHYDROBIOPTERIN, ACETATE ION, ARGININE, ...
Authors:	Li, H, Igarashi, J, Jamal, J, Yang, W, Poulos, T.L.
Deposit date:	2006-02-24
Release date:	2006-08-08
Last modified:	2023-08-30
Method:	X-RAY DIFFRACTION (2 Å)
Cite:	Structural studies of constitutive nitric oxide synthases with diatomic ligands bound. J.Biol.Inorg.Chem., 11, 2006

2G8H

B. halodurans RNase H catalytic domain D192N mutant in complex with Mg2+ and RNA/DNA hybrid (non-P nick at the active site)
Descriptor:	5'-D(APTPGPTPCPG)-3', 5'-R(UPCPGPAPCPA)-3', MAGNESIUM ION, ...
Authors:	Nowotny, M, Yang, W.
Deposit date:	2006-03-02
Release date:	2006-04-25
Last modified:	2023-08-30
Method:	X-RAY DIFFRACTION (1.85 Å)
Cite:	Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. Embo J., 25, 2006

2G8K

B. halodurans RNase H catalytic domain D192N mutant in complex with Ca2+ and RNA/DNA hybrid (non-P nick at the active site)
Descriptor:	5'-D(APTPGPTPCPG)-3', 5'-R(UPCPGPAPCPA)-3', CALCIUM ION, ...
Authors:	Nowotny, M, Yang, W.
Deposit date:	2006-03-02
Release date:	2006-04-25
Last modified:	2023-08-30
Method:	X-RAY DIFFRACTION (1.65 Å)
Cite:	Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. Embo J., 25, 2006

7SGL

DNA-PK complex of DNA end processing
Descriptor:	ADENOSINE-5'-TRIPHOSPHATE, DNA-dependent protein kinase catalytic subunit, Hairpin_1, ...
Authors:	Liu, L, Li, J, Chen, X, Yang, W, Gellert, M.
Deposit date:	2021-10-06
Release date:	2022-01-12
Last modified:	2022-01-19
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	Autophosphorylation transforms DNA-PK from protecting to processing DNA ends. Mol.Cell, 82, 2022

6V0V

Cryo-EM structure of mouse WT RAG1/2 NFC complex (DNA0)
Descriptor:	CALCIUM ION, DNA (30-MER), V(D)J recombination-activating protein 1, ...
Authors:	Chen, X, Yang, W, Gellert, M.
Deposit date:	2019-11-19
Release date:	2020-01-29
Last modified:	2024-03-06
Method:	ELECTRON MICROSCOPY (3.61 Å)
Cite:	Cutting antiparallel DNA strands in a single active site. Nat.Struct.Mol.Biol., 27, 2020

6WYB

RTX (Reverse Transcription Xenopolymerase) in complex with an RNA/DNA hybrid
Descriptor:	1,2-ETHANEDIOL, 3,3',3''-phosphanetriyltripropanoic acid, DNA polymerase, ...
Authors:	Choi, W.S, He, P, Pothukuchy, A, Gollihar, J, Ellington, A.D, Yang, W.
Deposit date:	2020-05-12
Release date:	2020-08-19
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.5 Å)
Cite:	How a B family DNA polymerase has been evolved to copy RNA. Proc.Natl.Acad.Sci.USA, 117, 2020

6WYA

RTX (Reverse Transcription Xenopolymerase) in complex with a DNA duplex and dAMPNPP
Descriptor:	1,2-ETHANEDIOL, 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ...
Authors:	Choi, W.S, He, P, Pothukuchy, A, Gollihar, J, Ellington, A.D, Yang, W.
Deposit date:	2020-05-12
Release date:	2020-08-19
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.41 Å)
Cite:	How a B family DNA polymerase has been evolved to copy RNA. Proc.Natl.Acad.Sci.USA, 117, 2020

6OEO

Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1)
Descriptor:	CALCIUM ION, DNA (46-MER), DNA (57-MER), ...
Authors:	Chen, X, Cui, Y, Zhou, Z.H, Yang, W, Gellert, M.
Deposit date:	2019-03-27
Release date:	2020-01-29
Last modified:	2024-03-20
Method:	ELECTRON MICROSCOPY (3.69 Å)
Cite:	Cutting antiparallel DNA strands in a single active site. Nat.Struct.Mol.Biol., 27, 2020

6OEQ

Cryo-EM structure of mouse RAG1/2 12RSS-PRC/23RSS-NFC complex (DNA1)
Descriptor:	CALCIUM ION, DNA (46-MER), DNA (57-MER), ...
Authors:	Chen, X, Cui, Y, Zhou, Z.H, Yang, W, Gellert, M.
Deposit date:	2019-03-27
Release date:	2020-01-29
Last modified:	2024-03-20
Method:	ELECTRON MICROSCOPY (4.3 Å)
Cite:	Cutting antiparallel DNA strands in a single active site. Nat.Struct.Mol.Biol., 27, 2020

6OER

Cryo-EM structure of mouse RAG1/2 NFC complex (DNA2)
Descriptor:	CALCIUM ION, DNA (46-MER), DNA (57-MER), ...
Authors:	Chen, X, Cui, Y, Zhou, Z.H, Yang, W, Gellert, M.
Deposit date:	2019-03-27
Release date:	2020-01-29
Last modified:	2024-03-20
Method:	ELECTRON MICROSCOPY (3.29 Å)
Cite:	Cutting antiparallel DNA strands in a single active site. Nat.Struct.Mol.Biol., 27, 2020

6OES

Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain)
Descriptor:	CALCIUM ION, DNA (34-MER), DNA (35-MER), ...
Authors:	Chen, X, Cui, Y, Zhou, Z.H, Yang, W, Gellert, M.
Deposit date:	2019-03-27
Release date:	2020-01-22
Last modified:	2024-03-20
Method:	ELECTRON MICROSCOPY (3.06 Å)
Cite:	How mouse RAG recombinase avoids DNA transposition. Nat.Struct.Mol.Biol., 27, 2020

6OEM

Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0)
Descriptor:	DNA (46-MER), DNA (57-MER), High mobility group protein B1, ...
Authors:	Chen, X, Cui, Y, Zhou, Z.H, Yang, W, Gellert, M.
Deposit date:	2019-03-27
Release date:	2020-01-29
Last modified:	2020-02-26
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	Cutting antiparallel DNA strands in a single active site. Nat.Struct.Mol.Biol., 27, 2020

6OEP

Cryo-EM structure of mouse RAG1/2 12RSS-NFC/23RSS-PRC complex (DNA1)
Descriptor:	CALCIUM ION, DNA (46-MER), DNA (57-MER), ...
Authors:	Chen, X, Cui, Y, Zhou, Z.H, Yang, W, Gellert, M.
Deposit date:	2019-03-27
Release date:	2020-01-29
Last modified:	2024-03-13
Method:	ELECTRON MICROSCOPY (3.7 Å)
Cite:	Cutting antiparallel DNA strands in a single active site. Nat.Struct.Mol.Biol., 27, 2020

6OEN

Cryo-EM structure of mouse RAG1/2 PRC complex (DNA1)
Descriptor:	CALCIUM ION, DNA (46-MER), DNA (57-MER), ...
Authors:	Chen, X, Cui, Y, Zhou, Z.H, Yang, W, Gellert, M.
Deposit date:	2019-03-27
Release date:	2020-01-29
Last modified:	2020-02-26
Method:	ELECTRON MICROSCOPY (4.3 Å)
Cite:	Cutting antiparallel DNA strands in a single active site. Nat.Struct.Mol.Biol., 27, 2020

6OET

Cryo-EM structure of mouse RAG1/2 STC complex
Descriptor:	CALCIUM ION, DNA (30-MER), DNA (39-MER), ...
Authors:	Chen, X, Cui, Y, Zhou, Z.H, Yang, W, Gellert, M.
Deposit date:	2019-03-27
Release date:	2020-01-22
Last modified:	2024-03-20
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	How mouse RAG recombinase avoids DNA transposition. Nat.Struct.Mol.Biol., 27, 2020

1JXL

Crystal Structure of a Y-Family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide
Descriptor:	1,2-ETHANEDIOL, 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(GPGPGPGPGPAPAPGPGPAPTPT)-3', ...
Authors:	Ling, H, Boudsocq, F, Woodgate, R, Yang, W.
Deposit date:	2001-09-07
Release date:	2001-10-05
Last modified:	2023-08-16
Method:	X-RAY DIFFRACTION (2.1 Å)
Cite:	Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell(Cambridge,Mass.), 107, 2001

6OZH

Crystal structure of Ciona intestinalis (Ci) Endonuclease V in complex with a 24mer DNA containing an inosine followed by a ribo-adenosine
Descriptor:	CALCIUM ION, DNA/RNA (5'-D(PCPGPGPTPAPAPCPCPGPI)-R(PA)-D(PTPAPTPGPCPAPGPCPAPTPTPTPC)-3'), endonuclease V isoform X2
Authors:	Samara, N.L, Yang, W.
Deposit date:	2019-05-15
Release date:	2019-09-04
Last modified:	2024-03-13
Method:	X-RAY DIFFRACTION (3.026 Å)
Cite:	Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol.Cell, 76, 2019

6OZJ

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine in the absence of divalent cation
Descriptor:	1,2-ETHANEDIOL, DNA/RNA (5'-R(PCPGPGPUPAPAPCPCPC)-D(PI)-R(PAPUPAPUPGPCPAPUPGPCPAPUP*U)-3'), Endonuclease V, ...
Authors:	Samara, N.L, Yang, W.
Deposit date:	2019-05-15
Release date:	2019-09-04
Last modified:	2024-03-13
Method:	X-RAY DIFFRACTION (2.247 Å)
Cite:	Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol.Cell, 76, 2019

6OZQ

Crystal structure of Mus musculus (Mm) Endonuclease V (K155M) in complex with a 23mer RNA oligo containing an inosine after a 100 min soak in 10 mM Mn2+ and K+
Descriptor:	1,2-ETHANEDIOL, DNA/RNA (5'-R(PCPGPGPUPAPAPCPCPC)-D(PI)-R(PAPUPAPUPGPCPAPUPGPCPAPUP*U)-3'), Endonuclease V, ...
Authors:	Samara, N.L, Yang, W.
Deposit date:	2019-05-15
Release date:	2019-09-04
Last modified:	2024-03-13
Method:	X-RAY DIFFRACTION (2.153 Å)
Cite:	Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol.Cell, 76, 2019

6OZP

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 180 min soak in 10 mM Mn2+
Descriptor:	1,2-ETHANEDIOL, DNA/RNA (5'-R(CPGPGPUPAPAPCPCPC)-D(PI)-R(P*A)-3'), Endonuclease V, ...
Authors:	Samara, N.L, Yang, W.
Deposit date:	2019-05-15
Release date:	2019-09-04
Last modified:	2024-03-13
Method:	X-RAY DIFFRACTION (1.96 Å)
Cite:	Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol.Cell, 76, 2019

6OZE

Crystal structure of the catalytic domain of human Endonuclease V (C140S/C225S/C226A/C228S)
Descriptor:	ACETATE ION, Endonuclease V, GLYCEROL, ...
Authors:	Samara, N.L, Yang, W.
Deposit date:	2019-05-15
Release date:	2019-09-04
Last modified:	2023-10-11
Method:	X-RAY DIFFRACTION (1.5 Å)
Cite:	Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol.Cell, 76, 2019

6OZI

Crystal structure of Ciona intestinalis (Ci) Endonuclease V (D234N) in complex with a 23mer DNA containing an inosine followed by a ribo-adenosine
Descriptor:	DNA/RNA (23-MER), POTASSIUM ION, TRIETHYLENE GLYCOL, ...
Authors:	Samara, N.L, Yang, W.
Deposit date:	2019-05-15
Release date:	2019-09-04
Last modified:	2024-03-13
Method:	X-RAY DIFFRACTION (2.302 Å)
Cite:	Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol.Cell, 76, 2019

6OZS

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 90 min soak in 10 mM Mg2+
Descriptor:	1,2-ETHANEDIOL, DNA/RNA (5'-R(CPGPGPUPAPAPCPCPC)-D(PI)-R(P*A)-3'), Endonuclease V, ...
Authors:	Samara, N.L, Yang, W.
Deposit date:	2019-05-15
Release date:	2019-09-04
Last modified:	2024-03-13
Method:	X-RAY DIFFRACTION (2.41 Å)
Cite:	Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol.Cell, 76, 2019

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Total results:	434
Displayed results:	25
Sorted by:	Hit score (from highest)
Deposition authors:	"Yang, W."