7c0j

Crystal structure of chimeric mutant of GH5 in complex with Z-DNA

Method: X-RAY DIFFRACTION D_max: 52.3 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H5,Double-stranded RNA-specific adenosine deaminase

Gallus gallus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 25–64 Chain A； UniProt 76–88 Chain A； UniProt 92–93 Chain A； UniProt 95–98 Chain B； UniProt 25–64 Chain B； UniProt 76–88 Chain B； UniProt 92–93 Chain B； UniProt 95–98	Mutation：K41G,S42E,R43G,K53A,R95A	;DNA (5'-D(TPCPGPCPGPCP*G)-3') ; × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；MES pH 6.0, PEG 4000, ethylene glycol	Resolution 2.75 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7C0J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HST CRYSTAL STRUCTURE OF GLOBULAR DOMAIN OF HISTONE H5 AND ITS IMPLICATIONS FOR NUCLEOSOME BINDING Deposited 1993-03-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–108（90 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1HST CRYSTAL STRUCTURE OF GLOBULAR DOMAIN OF HISTONE H5 AND ITS IMPLICATIONS FOR NUCLEOSOME BINDING Deposited 1993-03-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 19–108（90 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
4QLC Crystal structure of chromatosome at 3.5 angstrom resolution Deposited 2014-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain U 23–99（77 aa）	Not recorded	CIT CITRIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.75；291 K；0.1 mM Citric acid, 0.1mM potassium chloride, and 10% MPD, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.50 Å R-free 0.243
5WCU Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Deposited 2017-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain U 23–98（76 aa） Fragment：UNP residues 23-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；0.1 M NH4NO3, 10% MPD (v/v)	Resolution 5.53 Å R-free 0.238
5WCU Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Deposited 2017-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain V 23–98（76 aa） Fragment：UNP residues 23-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；0.1 M NH4NO3, 10% MPD (v/v)	Resolution 5.53 Å R-free 0.238
7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric	Chain U 2–190（189 aa） Chain V 2–190（189 aa）	Not recorded	CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)	Resolution 2.84 Å R-free 0.259
8XJV Structural basis for the linker histone H5-nucleosome binding and chromatin compaction Deposited 2023-12-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 108 PDB declaration: 110-meric	Chain Ah 1–190（190 aa） Chain Ai 1–190（190 aa） Chain Aj 1–190（190 aa） Chain Ak 1–190（190 aa） Chain Al 1–190（190 aa） Chain Am 1–190（190 aa） Chain An 1–190（190 aa） Chain Ao 1–190（190 aa） Chain Ap 1–190（190 aa） Chain Aq 1–190（190 aa） Chain Ar 1–190（190 aa） Chain As 1–190（190 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.60 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H5_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–45； UniProt 25–64 Author chain A； PDBConstruct 56–68； UniProt 76–88 Author chain A； PDBConstruct 70–71； UniProt 92–93 Author chain A； PDBConstruct 73–76； UniProt 95–98 Author chain B； PDBConstruct 6–45； UniProt 25–64 Author chain B； PDBConstruct 56–68； UniProt 76–88 Author chain B； PDBConstruct 70–71； UniProt 92–93 Author chain B； PDBConstruct 73–76； UniProt 95–98

Histone H5,Double-stranded RNA-specific adenosine deaminase

Gallus gallus

UniProt P55265

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 169–178 Chain A； UniProt 192–192 Chain A； UniProt 195–195 Chain B； UniProt 169–178 Chain B； UniProt 192–192 Chain B； UniProt 195–195	Mutation：K41G,S42E,R43G,K53A,R95A	;DNA (5'-D(TPCPGPCPGPCP*G)-3') ; × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；MES pH 6.0, PEG 4000, ethylene glycol	Resolution 2.75 Å R-free 0.248

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7C0J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QBJ CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX Deposited 1999-04-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 133–209（77 aa） Fragment：N-TERMINAL HELIX-TURN-HELIX DOMAIN ZALPHA Chain B 133–209（77 aa） Fragment：N-TERMINAL HELIX-TURN-HELIX DOMAIN ZALPHA	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；HANGING DROP VAPOR DIFFUSION OVER 1.6 M (NH4)2SO4, 10 % GLYCEROL AT 24 DEGREES CELSIUS, pH 5.6	Resolution 2.10 Å R-free 0.265
1QBJ CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX Deposited 1999-04-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 133–209（77 aa） Fragment：N-TERMINAL HELIX-TURN-HELIX DOMAIN ZALPHA	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；HANGING DROP VAPOR DIFFUSION OVER 1.6 M (NH4)2SO4, 10 % GLYCEROL AT 24 DEGREES CELSIUS, pH 5.6	Resolution 2.10 Å R-free 0.265
1QGP NMR STRUCTURE OF THE Z-ALPHA DOMAIN OF ADAR1, 15 STRUCTURES Deposited 1999-05-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 125–201（77 aa） Fragment：Z-ALPHA DOMAIN	Mutation：C125S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) 0.137 M NACL；Pressure 1 NMR sample composition NA-PHOSPHATE	Resolution not provided
1XMK The Crystal structure of the Zb domain from the RNA editing enzyme ADAR1 Deposited 2004-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 294–366（73 aa）	Not recorded	CD CADMIUM ION × 2 NI NICKEL (II) ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；312 K；PEG1000, Cadmium Chloride, Nickel Chloride, Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 312K, pH 9.00	Resolution 0.97 Å R-free 0.183
2ACJ Crystal structure of the B/Z junction containing DNA bound to Z-DNA binding proteins Deposited 2005-07-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–202（63 aa） Fragment：Zalpha domain, ADAR1 Chain B 140–202（63 aa） Fragment：Zalpha domain, ADAR1 Chain C 140–202（63 aa） Fragment：Zalpha domain, ADAR1 Chain D 140–202（63 aa） Fragment：Zalpha domain, ADAR1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；22-23% MPD, 55-60mM sodium acetate, 15-16mM calsium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.60 Å R-free 0.285
2GXB Crystal Structure of The Za Domain bound to Z-RNA Deposited 2006-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 140–202（63 aa） Fragment：Za Domain Chain B 140–202（63 aa） Fragment：Za Domain	Not recorded	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；292 K；40% PEG600, 100mM Sodium Acetate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.25 Å R-free 0.244
2L54 Solution structure of the Zalpha domain mutant of ADAR1 (N43A,Y47A) Deposited 2010-10-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 136–198（63 aa） Fragment：DRADA 1 domain, UNP residues 136-198	Mutation：N43A, Y47A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR sample composition 50 mM sodium phosphate-1, 50 mM sodium chloride-2, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MDR Solution structure of the third double-stranded RNA-binding domain (dsRBD3) of human adenosine-deaminase ADAR1 Deposited 2013-09-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 708–801（94 aa） Fragment：UNP residues 708-801	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；313 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 0.7-0.9 mM [U-99% 13C; U-99% 15N] dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-0.9 mM [U-99% 13C; U-99% 15N] dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 100% D2O \| 100% D2O NMR sample composition 0.7-0.9 mM [U-99% 15N] dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-0.9 mM dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3F21 Crystal structure of Zalpha in complex with d(CACGTG) Deposited 2008-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209 Chain B 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.279
3F21 Crystal structure of Zalpha in complex with d(CACGTG) Deposited 2008-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.279
3F22 Crystal structure of Zalpha in complex with d(CGTACG) Deposited 2008-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209 Chain B 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.269
3F22 Crystal structure of Zalpha in complex with d(CGTACG) Deposited 2008-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.269
3F23 Crystal structure of Zalpha in complex with d(CGGCCG) Deposited 2008-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209 Chain B 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.264
3F23 Crystal structure of Zalpha in complex with d(CGGCCG) Deposited 2008-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.264
3IRQ Crystal structure of a Z-Z junction Deposited 2009-08-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–202（63 aa） Fragment：Zalpha domain Chain B 140–202（63 aa） Fragment：Zalpha domain Chain C 140–202（63 aa） Fragment：Zalpha domain Chain D 140–202（63 aa） Fragment：Zalpha domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；17% PEG 2000, 0.1 M Tris-HCl, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.271
3IRR Crystal Structure of a Z-Z junction (with HEPES intercalating) Deposited 2009-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–202（63 aa） Fragment：Zalpha domain Chain B 140–202（63 aa） Fragment：Zalpha domain Chain C 140–202（63 aa） Fragment：Zalpha domain Chain D 140–202（63 aa） Fragment：Zalpha domain	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；16% PEG 2000 MME, 0.1 M HEPES, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.65 Å R-free 0.283
5ZU1 Crystal Structure of BZ junction in diverse sequence Deposited 2018-05-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–198（59 aa） Chain B 140–198（59 aa） Chain C 140–198（59 aa） Chain D 140–198（59 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 4.5；296 K；25% 2-methyl-2,4-pentanediol (MPD), 100mM NaOAC, pH 4.5	Resolution 3.01 Å R-free 0.280
5ZUO Crystal Structure of BZ junction in diverse sequence Deposited 2018-05-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–202（63 aa） Chain B 140–202（63 aa） Chain C 140–202（63 aa） Chain D 140–202（63 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.5；296 K；20% dioxane, with microseeding of small crystals	Resolution 2.90 Å R-free 0.301
5ZUP Crystal Structure of BZ junction in diverse sequence Deposited 2018-05-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–202（63 aa） Chain B 140–202（63 aa） Chain C 140–202（63 aa） Chain D 140–202（63 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.5；296 K；25% ethylene glycol, with microseeding of small crystal	Resolution 2.90 Å R-free 0.282
7C0I Crystal structure of chimeric mutant of E3L in complex with Z-DNA Deposited 2020-05-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 169–184（16 aa） Chain A 192–193（2 aa） Chain A 195–195（1 aa） Chain B 169–184（16 aa） Chain B 192–193（2 aa） Chain B 195–195（1 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；295 K；Sodium citrate pH 4.0, Ammonium sulfate, ethylene glycol	Resolution 2.40 Å R-free 0.227
7C0I Crystal structure of chimeric mutant of E3L in complex with Z-DNA Deposited 2020-05-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 169–184（16 aa） Chain C 192–193（2 aa） Chain C 195–195（1 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；295 K；Sodium citrate pH 4.0, Ammonium sulfate, ethylene glycol	Resolution 2.40 Å R-free 0.227
7ZJ1 Crystal structure of ADAR1-dsRBD3 dimer Deposited 2022-04-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 716–797（82 aa） Chain B 716–797（82 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；100 mM sodium citrate pH 4.0, 20% (w/v) PEG 6000, and 1.0 M LiCl	Resolution 1.65 Å R-free 0.225
7ZLQ Crystal structure of ADAR1-dsRBD3 dimer in complex with dsRNA Deposited 2022-04-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 716–797（82 aa） Chain B 716–797（82 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM sodium cacodylate, 5% (w/v) PEG 4000, 30 mM CaCl2, 230 mM KCl	Resolution 2.80 Å R-free 0.266
8GBC Homo sapiens Zalpha mutant - N173S Deposited 2023-02-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 140–202（63 aa）	Mutation：N173S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；277 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 2 mM [U-13C; U-15N] protein, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
8GBD Homo sapiens Zalpha mutant - P193A Deposited 2023-02-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 140–202（63 aa）	Mutation：P193A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；277 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 2 mM [U-13C; U-15N] protein, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
9B83 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from human GLI1 gene Deposited 2024-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 127–1226（1100 aa） Chain B 127–1226（1100 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9B84 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from HT2C gene Deposited 2024-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 127–1226（1100 aa） Chain B 127–1226（1100 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B89 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from HT2C gene in the pre-editing state Deposited 2024-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 127–1226（1100 aa） Chain B 127–1226（1100 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.87 Å

23 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DSRAD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 46–55； UniProt 169–178 Author chain A； PDBConstruct 69–69； UniProt 192–192 Author chain A； PDBConstruct 72–72； UniProt 195–195 Author chain B； PDBConstruct 46–55； UniProt 169–178 Author chain B； PDBConstruct 69–69； UniProt 192–192 Author chain B； PDBConstruct 72–72； UniProt 195–195

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7c0j
Deposition date deposition_date	2020-05-01
Structure title title	Crystal structure of chimeric mutant of GH5 in complex with Z-DNA
Keywords keywords	GH5, Protein-DNA complex, protein engineering, Z-DNA binding protein, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.35 Å
Radius of gyration Rg (electron density) rg_electron	19.01 Å
Forward intensity I(0) i0	6683840.00
Molecular weight molecular_weight	16810.0 kDa
Excluded volume excluded_volume	20104 Å³
Envelope volume envelope_volume	25142 Å³
Hydration-shell volume shell_volume	12352 Å³
Envelope diameter envelope_diameter	63.0 Å
Shell Rg shell_rg	22.88 Å
Envelope Rg envelope_rg	19.27 Å
Shape Rg shape_rg	19.06 Å
Total Rg total_rg	19.46 Å
Total atoms total_atoms	1169
Residues n_residues	133
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	52.3 Å
Rg (real space) rg_real	17.57 Å
Rg uncertainty (real space) rg_real_error	0.11 Å
I(0) (real space) i0_real	6.4400e+06
I(0) uncertainty (real space) i0_real_error	5.3970e+04
Rg (reciprocal space) rg_reciprocal	18.53 Å
I(0) (reciprocal space) i0_reciprocal	6684000.0000
Solution quality estimate total_estimate	0.6678
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.521
Kurtosis Kurtosis kurtosis	-0.244
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	3.5730
Highest regularization parameter α highest_alpha	1196000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 0.987; Sysdev: 0.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Histone H5,Double-stranded RNA-specific adenosine deaminase
Molecular weight formula_weight	8109.3 kDa
Mutation mutation	K41G,S42E,R43G,K53A,R95A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1179

GSHMASHPTYSEMIAAAIRAEGEGGGSSRQSIQAYIKSHYKVGHNKKEINRVLYSLLAAGVLKQTKGVPGSWALAK

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	Chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPCPGPCPGPCP*G)-3') ;
Molecular weight formula_weight	2114.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,E

TCGCGCG

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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8. Citations (1)

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Unit-cell length a length_a	31.135 Å
Unit-cell length b length_b	47.305 Å
Unit-cell length c length_c	57.118 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	28.876 Å
R factor r_factor	0.2243
R_work r_work	0.2229
R_free r_free	0.2482

fit	/app/data/saxs_computation/c0/7c0j/7c0j.fit
pddf	/app/data/pr_computation/c0/7c0j/7c0j.pr.out
profile	/app/data/saxs_computation/c0/7c0j/7c0j.dat

Crystal structure of chimeric mutant of GH5 in complex with Z-DNA

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H5,Double-stranded RNA-specific adenosine deaminase

State in the Current Structure

Other States of the Same Protein in the Database

Histone H5,Double-stranded RNA-specific adenosine deaminase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)