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- PDB-6nzu: Structure of the human frataxin-bound iron-sulfur cluster assembl... -

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Entry
Database: PDB / ID: 6nzu
TitleStructure of the human frataxin-bound iron-sulfur cluster assembly complex
Components
  • Acyl carrier protein
  • Cysteine desulfurase, mitochondrial
  • Frataxin, mitochondrial
  • Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
  • LYR motif-containing protein 4
KeywordsTRANSFERASE / OXIDOREDUCTASE / human frataxin-bound iron-sulfur cluster assembly complex
Function / homology
Function and homology information


: / negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / proprioception / Molybdenum cofactor biosynthesis / positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / : / L-cysteine desulfurase complex / iron incorporation into metallo-sulfur cluster ...: / negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / proprioception / Molybdenum cofactor biosynthesis / positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / : / L-cysteine desulfurase complex / iron incorporation into metallo-sulfur cluster / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / iron chaperone activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone / Maturation of TCA enzymes and regulation of TCA cycle / cysteine desulfurase / cysteine desulfurase activity / negative regulation of organ growth / positive regulation of catalytic activity / mitochondrial respiratory chain complex III assembly / Mo-molybdopterin cofactor biosynthetic process / Mitochondrial protein import / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / oxidative phosphorylation / response to iron ion / embryo development ending in birth or egg hatching / [2Fe-2S] cluster assembly / adult walking behavior / heme biosynthetic process / negative regulation of multicellular organism growth / organ growth / muscle cell cellular homeostasis / iron-sulfur cluster assembly / ferroxidase / negative regulation of release of cytochrome c from mitochondria / acyl carrier activity / ferroxidase activity / protein autoprocessing / iron-sulfur cluster binding / ferric iron binding / ferrous iron binding / 2 iron, 2 sulfur cluster binding / cellular response to hydrogen peroxide / pyridoxal phosphate binding / iron ion transport / Maturation of replicase proteins / positive regulation of cell growth / molecular adaptor activity / intracellular iron ion homeostasis / nuclear body / mitochondrial matrix / iron ion binding / positive regulation of cell population proliferation / centrosome / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Frataxin/CyaY / LYRM4, LYR domain / : / Sufe protein. Chain: A - #10 / Frataxin / Sufe protein. Chain: A / ISC system FeS cluster assembly, IscU scaffold / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site ...Frataxin/CyaY / LYRM4, LYR domain / : / Sufe protein. Chain: A - #10 / Frataxin / Sufe protein. Chain: A / ISC system FeS cluster assembly, IscU scaffold / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Cysteine desulfurase IscS / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Frataxin/CyaY superfamily / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8Q1 / PYRIDOXAL-5'-PHOSPHATE / Acyl carrier protein / Frataxin, mitochondrial / Iron-sulfur cluster assembly enzyme ISCU / LYR motif-containing protein 4 / Cysteine desulfurase
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFox, N.G. / Yu, X. / Xidong, F. / Alain, M. / Joseph, N. / Claire, S.D. / Christine, B. / Han, S. / Yue, W.W.
CitationJournal: Nat Commun / Year: 2019
Title: Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism.
Authors: Nicholas G Fox / Xiaodi Yu / Xidong Feng / Henry J Bailey / Alain Martelli / Joseph F Nabhan / Claire Strain-Damerell / Christine Bulawa / Wyatt W Yue / Seungil Han /
Abstract: The core machinery for de novo biosynthesis of iron-sulfur clusters (ISC), located in the mitochondria matrix, is a five-protein complex containing the cysteine desulfurase NFS1 that is activated by ...The core machinery for de novo biosynthesis of iron-sulfur clusters (ISC), located in the mitochondria matrix, is a five-protein complex containing the cysteine desulfurase NFS1 that is activated by frataxin (FXN), scaffold protein ISCU, accessory protein ISD11, and acyl-carrier protein ACP. Deficiency in FXN leads to the loss-of-function neurodegenerative disorder Friedreich's ataxia (FRDA). Here the 3.2 Å resolution cryo-electron microscopy structure of the FXN-bound active human complex, containing two copies of the NFS1-ISD11-ACP-ISCU-FXN hetero-pentamer, delineates the interactions of FXN with other component proteins of the complex. FXN binds at the interface of two NFS1 and one ISCU subunits, modifying the local environment of a bound zinc ion that would otherwise inhibit NFS1 activity in complexes without FXN. Our structure reveals how FXN facilitates ISC production through stabilizing key loop conformations of NFS1 and ISCU at the protein-protein interfaces, and suggests how FRDA clinical mutations affect complex formation and FXN activation.
History
DepositionFeb 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
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Revision 1.2Jul 10, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.3Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.1Apr 2, 2025Data content type: EM metadata
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Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Cysteine desulfurase, mitochondrial
B: LYR motif-containing protein 4
C: Acyl carrier protein
D: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
E: Cysteine desulfurase, mitochondrial
F: LYR motif-containing protein 4
G: Acyl carrier protein
H: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
I: Frataxin, mitochondrial
J: Frataxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,43816
Polymers183,73110
Non-polymers1,7066
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area27520 Å2
ΔGint-184 kcal/mol
Surface area62340 Å2

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Components

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Protein , 5 types, 10 molecules AEBFCGDHIJ

#1: Protein Cysteine desulfurase, mitochondrial


Mass: 44850.371 Da / Num. of mol.: 2 / Fragment: UNP residues 56-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFS1, NIFS, HUSSY-08
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Y697, cysteine desulfurase
#2: Protein LYR motif-containing protein 4


Mass: 10850.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYRM4, C6orf149, ISD11, CGI-203
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9HD34
#3: Protein Acyl carrier protein / ACP


Mass: 8251.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acpP, DQL48_09575, EOL36_14065
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A437HBF4
#4: Protein Iron-sulfur cluster assembly enzyme ISCU, mitochondrial / NifU-like N-terminal domain-containing protein / NifU-like protein


Mass: 13412.580 Da / Num. of mol.: 2 / Fragment: UNP residues 35-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISCU, NIFUN
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9H1K1
#5: Protein Frataxin, mitochondrial / Friedreich ataxia protein / Fxn


Mass: 14501.001 Da / Num. of mol.: 2 / Fragment: UNP residues 81-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FXN, FRDA, X25
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q16595, ferroxidase

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Non-polymers , 3 types, 6 molecules

#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H45N2O8PS
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The human frataxin-bound iron-sulfur cluster assembly complex
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.186 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 42 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
8UCSF Chimeramodel fitting
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267153 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
15KZ5

5kz5

A5KZ51
25WKP

5wkp

A5WKP2
35WKP

5wkp

B5WKP2
45WKP

5wkp

C5WKP2
55WKP

5wkp

D5WKP2

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