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1ly7

The solution structure of the the c-terminal domain of frataxin, the protein responsible for friedreich ataxia

Method: SOLUTION NMR Dmax: 51.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

frataxin

Homo sapiens

UniProt Q16595

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 91–210 Fragment：C-TERMINAL DOMAIN (91-210) No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；300 K；Ionic strength (raw mmCIF value) 10 mM phosphate；Pressure ambient NMR sample composition：1 MM FRATAXIN. U-15N 10 MM PHOSPHATE BUFFER (PH 6.8)90% H2O, 10% D2O | h2o Resolution not provided

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 1LY7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EKG MATURE HUMAN FRATAXIN Deposited 2000-03-08 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 84–210（127 aa） Fragment：RESIDUES 88-210
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；2.5 M ammonium sulfate, 0.1 sodium citrate, 2% sucrose, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Resolution 1.80 Å R-free 0.220
3S4M Crystal structure of wild-type human frataxin Deposited 2011-05-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；30% MPD, 0.1 M sodium citrate, 0.2 M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.30 Å R-free 0.187
3S5D Crystal structure of human frataxin variant W155A Deposited 2011-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：W155A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；1.8 M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.50 Å R-free 0.192
3S5E Crystal structure of human frataxin variant W155R, one of the Friedreich's ataxia point mutations Deposited 2011-05-23 Different construct Different mutation/modification 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 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：W155R MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；16% PEG2000 MME, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.31 Å R-free 0.197
3S5F Crystal structure of human frataxin variant W155F Deposited 2011-05-23 Different construct Different mutation/modification 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 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：W155F MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.2 M sodium acetate trihydrate, 0.1 M Tris hydrochloride, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.50 Å R-free 0.213
3S5F Crystal structure of human frataxin variant W155F Deposited 2011-05-23 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：W155F MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.2 M sodium acetate trihydrate, 0.1 M Tris hydrochloride, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.50 Å R-free 0.213
3T3J 1.70 A structure of Friedreich's ataxia frataxin variant N146K Deposited 2011-07-25 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：N146K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；28% PEG2000 MME, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.245
3T3K 1.24 A Structure of Friedreich's ataxia frataxin variant Q148R Deposited 2011-07-25 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q148R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG3000, 0.1 M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.24 Å R-free 0.197
3T3L 1.15 A structure of human frataxin variant Q153A Deposited 2011-07-25 Different construct Different mutation/modification 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 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q153A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；2.0 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.2 M potassium sodium tartrate tetrahydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.15 Å R-free 0.179
3T3T 1.38 A structure of human frataxin variant Q148G Deposited 2011-07-25 Different construct Different mutation/modification 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 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q148G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；2.0 M ammonium sulfate, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.38 Å R-free 0.227
3T3T 1.38 A structure of human frataxin variant Q148G Deposited 2011-07-25 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q148G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；2.0 M ammonium sulfate, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.38 Å R-free 0.227
3T3T 1.38 A structure of human frataxin variant Q148G Deposited 2011-07-25 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q148G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；2.0 M ammonium sulfate, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.38 Å R-free 0.227
3T3T 1.38 A structure of human frataxin variant Q148G Deposited 2011-07-25 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q148G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；2.0 M ammonium sulfate, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.38 Å R-free 0.227
3T3X 1.57 A structure of Friedreich's ataxia frataxin variant R165C Deposited 2011-07-25 Different construct Different mutation/modification 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 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：R165C SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；1.9 M ammonium sulfate, 0.1 M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.57 Å R-free 0.251
3T3X 1.57 A structure of Friedreich's ataxia frataxin variant R165C Deposited 2011-07-25 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：R165C SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；1.9 M ammonium sulfate, 0.1 M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.57 Å R-free 0.251
5KZ5 Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery: the Complex Formed by the Iron Donor, the Sulfur Donor, and the Scaffold Deposited 2016-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain A 42–210（169 aa）
Chain B 42–210（169 aa）
Chain C 42–210（169 aa）
Chain D 42–210（169 aa）
Chain E 42–210（169 aa）
Chain F 42–210（169 aa）
Chain G 42–210（169 aa）
Chain H 42–210（169 aa）
Chain I 42–210（169 aa）
Chain J 42–210（169 aa）
Chain K 42–210（169 aa）
Chain L 42–210（169 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 14.30 Å
6NZU Structure of the human frataxin-bound iron-sulfur cluster assembly complex Deposited 2019-02-14 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 × 10 PDB declaration: decameric
Chain I 81–210（130 aa） Fragment：UNP residues 81-210
Chain J 81–210（130 aa） Fragment：UNP residues 81-210
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8PK8 Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (persulfide on ISCU2) Deposited 2023-06-26 Different construct 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 E 81–210（130 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 FE2 FE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
8PK9 Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (persulfide on NFS1 and ISCU2) Deposited 2023-06-26 Different construct 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 E 81–210（130 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 FE2 FE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
8RME Structure of the core ISC complex under turnover conditions (frataxin-bound) Deposited 2024-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain I 81–210（130 aa）
Not recorded FE2 FE (II) ION × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9HO4 Crystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 6B1 Deposited 2024-12-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 93–206（114 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M HEPES pH 7.0 0.8M Potassium Sodium Tartrate
Resolution 1.76 Å R-free 0.175
9HO5 Crystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 4A7 Deposited 2024-12-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 90–210（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium Thiocyanate pH 6.9 20% PEG 3350
Resolution 1.50 Å R-free 0.210
9HO6 Crystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 16C10 Deposited 2024-12-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 90–210（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；15% PEG 10K 0.1M Ammonium acetate 0.1M Bis-Tris pH 5.5
Resolution 2.00 Å R-free 0.227
9HO6 Crystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 16C10 Deposited 2024-12-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 90–210（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；15% PEG 10K 0.1M Ammonium acetate 0.1M Bis-Tris pH 5.5
Resolution 2.00 Å R-free 0.227

18 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FRDA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–121； UniProt 91–210

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 1ly7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ly7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ly7
Deposition date deposition_date2002-06-07
Structure title titleThe solution structure of the the c-terminal domain of frataxin, the protein responsible for friedreich ataxia
Keywords keywordsalpha-beta, UNKNOWN FUNCTION; UNKNOWN FUNCTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.56 Å
Radius of gyration Rg (electron density) rg_electron13.97 Å
Forward intensity I(0) i0552863000.00
Molecular weight molecular_weight202260.0 kDa
Excluded volume excluded_volume253840 ų
Envelope volume envelope_volume27926 ų
Hydration-shell volume shell_volume14986 ų
Envelope diameter envelope_diameter58.0 Å
Shell Rg shell_rg21.68 Å
Envelope Rg envelope_rg16.09 Å
Shape Rg shape_rg13.93 Å
Total Rg total_rg14.30 Å
Total atoms total_atoms28085
Residues n_residues1815
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 dmax51.8 Å
Rg (real space) rg_real14.51 Å
Rg uncertainty (real space) rg_real_error0.32 Å
I(0) (real space) i0_real5.5290e+08
I(0) uncertainty (real space) i0_real_error6.6240e+06
Rg (reciprocal space) rg_reciprocal14.51 Å
I(0) (reciprocal space) i0_reciprocal552900000.0000
Solution quality estimate total_estimate0.7554
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.7 Å
Skewness Skewness skewness0.248
Kurtosis Kurtosis kurtosis-0.091
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha399600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.608; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ly7a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.82 — N domain of copper amine oxidase-like
Superfamily Superfamily superfamilyd.82.2 — Frataxin/Nqo15-like
Family Family familyd.82.2.1 — Frataxin-like
Domain ID domain_idd1ly7a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1ly7A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology920 — Metal Transport, Frataxin; Chain A
Homologous superfamily homologous superfamily10 — Frataxin/CyaY
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8. Citations (2)

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9. Files and Curves (10)