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2yvi

Crystal structure of a death domain of human ankryn protein

Method: X-RAY DIFFRACTION Dmax: 43.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ankyrin-1

Homo sapiens

UniProt P16157

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1394–1497 Fragment：UNP residues 1394-1497, death domain GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2M NaCl, 0.1M TrisCl pH8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 1.92 Å R-free 0.217
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1394–1497 Fragment：UNP residues 1394-1497, death domain GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2M NaCl, 0.1M TrisCl pH8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 1.92 Å R-free 0.217

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 2YVI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1N11 D34 REGION OF HUMAN ANKYRIN-R AND LINKER Deposited 2002-10-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 402–827（426 aa） Fragment：D34 region
Not recorded BR BROMIDE ION × 1 CL CHLORIDE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG400, HEPES, NaBr, CaCl2, acetonitrile, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.303
2YQF Solution structure of the death domain of Ankyrin-1 Deposited 2007-03-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1394–1497（104 aa） Fragment：death domain, UNP residues 1394-1497
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
3F59 Crystal structure of ZU5-ANK, the spectrin binding region of human erythroid ankyrin Deposited 2008-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 911–1068（158 aa） Fragment：ZU5-ANK, spectrin binding region of human erythroid ankyrin: UNP residues 911-1068
Not recorded BR BROMIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；20% PEG 4000, 0.25 M KBr, 10 mM DTT, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.00 Å R-free 0.264
3F59 Crystal structure of ZU5-ANK, the spectrin binding region of human erythroid ankyrin Deposited 2008-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 911–1068（158 aa） Fragment：ZU5-ANK, spectrin binding region of human erythroid ankyrin: UNP residues 911-1068
Not recorded BR BROMIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；20% PEG 4000, 0.25 M KBr, 10 mM DTT, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.00 Å R-free 0.264
3F59 Crystal structure of ZU5-ANK, the spectrin binding region of human erythroid ankyrin Deposited 2008-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 911–1068（158 aa） Fragment：ZU5-ANK, spectrin binding region of human erythroid ankyrin: UNP residues 911-1068
Not recorded BR BROMIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；20% PEG 4000, 0.25 M KBr, 10 mM DTT, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.00 Å R-free 0.264
3F59 Crystal structure of ZU5-ANK, the spectrin binding region of human erythroid ankyrin Deposited 2008-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 911–1068（158 aa） Fragment：ZU5-ANK, spectrin binding region of human erythroid ankyrin: UNP residues 911-1068
Not recorded BR BROMIDE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；20% PEG 4000, 0.25 M KBr, 10 mM DTT, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.00 Å R-free 0.264
3KBT Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK) Deposited 2009-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 911–1068（158 aa） Fragment：UNP residues 911-1068
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.75 Å R-free 0.292
3KBT Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK) Deposited 2009-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 911–1068（158 aa） Fragment：UNP residues 911-1068
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.75 Å R-free 0.292
3KBU Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK), EMTS derivative Deposited 2009-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 911–1068（158 aa） Fragment：UNP residues 911-1068
Not recorded HG MERCURY (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.75 Å R-free 0.277
3KBU Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK), EMTS derivative Deposited 2009-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 911–1068（158 aa） Fragment：UNP residues 911-1068
Not recorded HG MERCURY (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.75 Å R-free 0.277
3UD1 Crystal structure of ZU5A-ZU5B domains of human erythrocyte ankyrin Deposited 2011-10-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 911–1233（323 aa） Fragment：ZU5A-ZU5B Ankyrin-R, UNP residues 911-1233
Not recorded EOH ETHANOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；283.15 K；25% ethanol, 0.1 M Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K
Resolution 2.00 Å R-free 0.206
3UD1 Crystal structure of ZU5A-ZU5B domains of human erythrocyte ankyrin Deposited 2011-10-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 911–1233（323 aa） Fragment：ZU5A-ZU5B Ankyrin-R, UNP residues 911-1233
Not recorded EOH ETHANOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；283.15 K；25% ethanol, 0.1 M Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K
Resolution 2.00 Å R-free 0.206
3UD1 Crystal structure of ZU5A-ZU5B domains of human erythrocyte ankyrin Deposited 2011-10-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 911–1233（323 aa） Fragment：ZU5A-ZU5B Ankyrin-R, UNP residues 911-1233
Not recorded EOH ETHANOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；283.15 K；25% ethanol, 0.1 M Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K
Resolution 2.00 Å R-free 0.206
3UD2 Crystal structure of Selenomethionine ZU5A-ZU5B protein domains of human erythrocyte ankyrin Deposited 2011-10-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 911–1233（323 aa） Fragment：SeMet ZU5A-ZU5B Ankyrin-R,UNP residues 911-1233
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 EOH ETHANOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；283.15 K；25% ethanol, 0.1 M Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K
Resolution 2.21 Å R-free 0.259
3UD2 Crystal structure of Selenomethionine ZU5A-ZU5B protein domains of human erythrocyte ankyrin Deposited 2011-10-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 911–1233（323 aa） Fragment：SeMet ZU5A-ZU5B Ankyrin-R,UNP residues 911-1233
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 16 EOH ETHANOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；283.15 K；25% ethanol, 0.1 M Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K
Resolution 2.21 Å R-free 0.259
3UD2 Crystal structure of Selenomethionine ZU5A-ZU5B protein domains of human erythrocyte ankyrin Deposited 2011-10-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 911–1233（323 aa） Fragment：SeMet ZU5A-ZU5B Ankyrin-R,UNP residues 911-1233
Non-standard monomer：Yes (specific site not provided by mmCIF) EOH ETHANOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；283.15 K；25% ethanol, 0.1 M Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K
Resolution 2.21 Å R-free 0.259
7TW3 Cryo-EM structure of human ankyrin complex (B2P1A1) from red blood cell Deposited 2022-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–1881（1881 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7TW5 Cryo-EM structure of human ankyrin complex (B2P1A2) from red blood cell Deposited 2022-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain G 1–1881（1881 aa）
Chain H 1–1881（1881 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
7TW6 Cryo-EM structure of human ankyrin complex (B4P1A1) from red blood cell Deposited 2022-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 1–1881（1881 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
7UZQ Local refinement of RhAG-RhCE-ANK1(AR1-5), from consensus refinement of all classes Deposited 2022-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–201（201 aa） Fragment：AR1-5 (UNP residues 1-201)
Not recorded CLR CHOLESTEROL × 2 AJP Digitonin × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL and 0.01% ( w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds
Resolution 2.17 Å
7UZU Ankyrin-1 (N-terminal region of membrane binding domain, local refinement from consensus reconstruction; bound to N-terminal peptide from band 3) Deposited 2022-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1881（1881 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL and 0.01% ( w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds
Resolution 2.30 Å
7V0K Consensus refinement of human erythrocyte ankyrin-1 complex (Composite map) Deposited 2022-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–1881（1881 aa）
Not recorded CLR CHOLESTEROL × 6 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds
Resolution 2.40 Å
7V0M Local refinement of ankyrin-1 (N-terminal half), class 1 of erythrocyte ankyrin-1 complex Deposited 2022-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1881（1881 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds
Resolution 2.70 Å
7V0S Local refinement of RhAG/CE trimer, class 1 of erythrocyte ankyrin-1 complex Deposited 2022-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–1881（1881 aa）
Not recorded CLR CHOLESTEROL × 2 AJP Digitonin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds
Resolution 2.50 Å
7V0X Local refinement of ankyrin-1 (C-terminal half), class 1 of erythrocyte ankyrin-1 complex Deposited 2022-05-11 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 1–1881（1881 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds.
Resolution 3.00 Å
8CS9 Composite reconstruction of Class 1 of the erythrocyte ankyrin-1 complex Deposited 2022-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 1–1881（1881 aa）
Not recorded CLR CHOLESTEROL × 8 AJP Digitonin × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds
Resolution 2.74 Å
8CSL Sub-tomogram averaging of erythrocyte ankyrin-1 complex Deposited 2022-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain A 1–1881（1881 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；130 mM KCl, 10 mM HEPES, pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 25.00 Å
8CSV Local refinement of Anykyrin-1 (N-terminal half of membrane binding domain) in Class 2 of erythrocyte ankyrin-1 complex Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1881（1881 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds
Resolution 2.70 Å
8CTE Class 2 of erythrocyte ankyrin-1 complex (Composite map) Deposited 2022-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 1–1881（1881 aa）
Not recorded CLR CHOLESTEROL × 10 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification.
cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds
Resolution 2.90 Å

20 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ANK1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–111； UniProt 1394–1497

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

SAXS profile for 2yvi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2yvi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2yvi
Deposition date deposition_date2007-04-12
Structure title titleCrystal structure of a death domain of human ankryn protein
Keywords keywords;homo sapiens, death domain, monomer, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, CELL ADHESION ;; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.12 Å
Radius of gyration Rg (electron density) rg_electron12.54 Å
Forward intensity I(0) i02338190.00
Molecular weight molecular_weight10138.0 kDa
Excluded volume excluded_volume12584 ų
Envelope volume envelope_volume14170 ų
Hydration-shell volume shell_volume9856 ų
Envelope diameter envelope_diameter43.8 Å
Shell Rg shell_rg17.94 Å
Envelope Rg envelope_rg12.87 Å
Shape Rg shape_rg12.52 Å
Total Rg total_rg13.88 Å
Total atoms total_atoms710
Residues n_residues89
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax43.8 Å
Rg (real space) rg_real14.02 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real2.3380e+06
I(0) uncertainty (real space) i0_real_error2.3840e+04
Rg (reciprocal space) rg_reciprocal14.03 Å
I(0) (reciprocal space) i0_reciprocal2338000.0000
Solution quality estimate total_estimate0.8199
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.7 Å
Skewness Skewness skewness0.124
Kurtosis Kurtosis kurtosis-0.335
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha323600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; 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)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2yviA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology533 — Death Domain, Fas
Homologous superfamily homologous superfamily10 — Death Domain, Fas
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