8ZZF | pdb_00008zzf

Structure of human mitochondrial iron sulfur cluster core complex (NIAUF)2

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.

PDB DOI: https://doi.org/10.2210/pdb8ZZF/pdb

Organism(s): Homo sapiens, Escherichia coli (strain K12)
Mutation(s): No

Deposited: 2018-01-24 Released: 2018-06-08
Deposition Author(s): Cai, K., Frederick, R.O., Dashti, H., Markley, J.L.

Integrative Structure Snapshot

Multi-Scale: No
Multi-State: No
Ordered-State: No
Deposited Models: 1
Representative Model: 1

wwPDB ValidationFull ReportSummary Report

This is version 1.0 of the entry. See complete history.

Literature

Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small Angle X-ray Scattering

Cai, K., Frederick, R.O., Dashti, H., Markley, J.L.

(2018) Structure 26: 1127-1136

PubMed: 29983374 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.str.2018.05.017
Primary Citation of Related Structures:
8ZZF

PubMed Abstract:
Cysteine desulfurase plays a central role in mitochondrial iron-sulfur cluster biogenesis by generating sulfur through the conversion of L-cysteine to L-alanine and by serving as the platform for assembling other components of the biosynthetic machinery, including ISCU, frataxin, and ferredoxin. The human mitochondrial cysteine desulfurase complex consists of two copies each of NFS1, ISD11, and acyl carrier protein. We describe results from chemical crosslinking coupled with tandem mass spectrometry and small-angle X-ray scattering studies that are consistent with a closed NFS1 dimer rather than an open one for both the cysteine desulfurase-ISCU and cysteine desulfurase-ISCU-frataxin complexes. We present a structural model for the cysteine desulfurase-ISCU-frataxin complex derived from chemical crosslinking restraints in conjunction with the recent crystal structure of the cysteine desulfurase-ISCU-zinc complex and distance constraints from nuclear magnetic resonance.

Organizational Affiliation

Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.

Macromolecule Content

Total Structure Weight: 189.21 kDa
Atom Count: 11,745
Modeled Residue Count: 1,595
Deposited Residue Count: 1,686
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NFS1	A, E	406	Homo sapiens	Mutation(s): 0 Gene Names: NFS1 EC: 2.8.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y697 (Homo sapiens) Explore Q9Y697 Go to UniProtKB: Q9Y697
PHAROS: Q9Y697 GTEx: ENSG00000244005
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y697
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ISD11	B, F	91	Homo sapiens	Mutation(s): 0 Gene Names: LYRM4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD34 (Homo sapiens) Explore Q9HD34 Go to UniProtKB: Q9HD34
PHAROS: Q9HD34 GTEx: ENSG00000214113
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HD34
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acp	C, G	77	Escherichia coli (strain K12)	Mutation(s): 0 Gene Names: acpP
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8 Go to UniProtKB: P0A6A8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6A8
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ISCU	D, H	150	Homo sapiens	Mutation(s): 0 Gene Names: ISCU
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1K1 (Homo sapiens) Explore Q9H1K1 Go to UniProtKB: Q9H1K1
PHAROS: Q9H1K1 GTEx: ENSG00000136003
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H1K1
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
FXN	I, J	119	Homo sapiens	Mutation(s): 0 Gene Names: FXN EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16595 (Homo sapiens) Explore Q16595 Go to UniProtKB: Q16595
PHAROS: Q16595 GTEx: ENSG00000165060
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16595
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8Q1 Query on 8Q1 Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain O [auth G] MOL2 format, chain L [auth C] MOL2 format, chain O [auth G] mmCIF format, chain L [auth C] mmCIF format, chain O [auth G]	L [auth C], O [auth G]	S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate C₂₃ H₄₅ N₂ O₈ P S MVHUOSAYFQKAMT-NRFANRHFSA-N		Interactions Focus chain L [auth C] Focus chain O [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain P [auth H] MOL2 format, chain M [auth D] MOL2 format, chain P [auth H] mmCIF format, chain M [auth D] mmCIF format, chain P [auth H]	M [auth D], P [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain P [auth H]