6WI2

Structure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.coli ACP1 at 1.95 A resolution (NIAU)2. N-terminal mutation of ISCU2 (L35) traps Nfs1 Cys loop in the active site of ISCU2 without metal present.

PDB DOI: https://doi.org/10.2210/pdb6WI2/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens, Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-04-08 Released: 2020-04-22
Deposition Author(s): Boniecki, M.T., Cygler, M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.185
R-Value Work: 0.150
R-Value Observed: 0.152

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The essential function of ISCU2 and its conserved N-terminus in Fe/S cluster biogenesis

Freibert, S.A., Boniecki, M.T., Shulz, V., Wilbrecht, C., Krapoth, N., Muhlenhoff, U., Stehling, O., Cygler, M., Lill, R.

To be published.

Macromolecule Content

Total Structure Weight: 85.75 kDa
Atom Count: 6,127
Modelled Residue Count: 686
Deposited Residue Count: 717
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase, mitochondrial	A	406	Homo sapiens	Mutation(s): 0 Gene Names: NFS1, NIFS, HUSSY-08 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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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYR motif-containing protein 4	B	91	Homo sapiens	Mutation(s): 1 Gene Names: LYRM4, C6orf149, ISD11, CGI-203
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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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	C	77	Escherichia coli	Mutation(s): 0
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
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial	D	143	Homo sapiens	Mutation(s): 0 Gene Names: ISCU, NIFUN
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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8Q1 Query on 8Q1 Download Ideal Coordinates CCD File SDF format, chain BB [auth C] MOL2 format, chain BB [auth C] mmCIF format, chain BB [auth C]	BB [auth C]	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 BB [auth C] Interactions & Density Focus chain BB [auth C]
EDT Query on EDT Download Ideal Coordinates CCD File SDF format, chain AB [auth B] MOL2 format, chain AB [auth B] mmCIF format, chain AB [auth B]	AB [auth B]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C₁₀ H₁₆ N₂ O₈ KCXVZYZYPLLWCC-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Interactions & Density Focus chain AB [auth B]
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain HB [auth D] MOL2 format, chain HB [auth D] mmCIF format, chain HB [auth D]	HB [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain HB [auth D] Interactions & Density Focus chain HB [auth D]
ETE Query on ETE Download Ideal Coordinates CCD File SDF format, chain DA [auth A] MOL2 format, chain DA [auth A] mmCIF format, chain DA [auth A]	DA [auth A]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₉ H₂₀ O₅ ZNYRFEPBTVGZDN-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Interactions & Density Focus chain DA [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain VA [auth B] MOL2 format, chain VA [auth B] mmCIF format, chain VA [auth B]	VA [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain VA [auth B] Interactions & Density Focus chain VA [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A]	X [auth A], Y [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain X [auth A] Focus chain Y [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain MA [auth A] MOL2 format, chain MA [auth A] mmCIF format, chain MA [auth A]	MA [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain MA [auth A] Interactions & Density Focus chain MA [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain GA [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain RA [auth A] SDF format, chain W [auth A] SDF format, chain YA [auth B] SDF format, chain Z [auth A] SDF format, chain OA [auth A] SDF format, chain QA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain W [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain QA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain W [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain QA [auth A]	EA [auth A] GA [auth A] I [auth A] J [auth A] OA [auth A] EA [auth A], GA [auth A], I [auth A], J [auth A], OA [auth A], QA [auth A], RA [auth A], W [auth A], YA [auth B], Z [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain GA [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain OA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain W [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Interactions & Density Focus chain EA [auth A] Focus chain GA [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain OA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain W [auth A] Focus chain YA [auth B] Focus chain Z [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain IB [auth D] SDF format, chain L [auth A] MOL2 format, chain H [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain L [auth A] mmCIF format, chain H [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain L [auth A]	H [auth A], IB [auth D], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain IB [auth D] Focus chain L [auth A] Interactions & Density Focus chain H [auth A] Focus chain IB [auth D] Focus chain L [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth D] SDF format, chain G [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain XA [auth B] SDF format, chain ZA [auth B] SDF format, chain GB [auth D] SDF format, chain JA [auth A] SDF format, chain V [auth A] SDF format, chain WA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain JA [auth A] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain JA [auth A] mmCIF format, chain V [auth A] mmCIF format, chain WA [auth B]	AA [auth A] BA [auth A] CA [auth A] CB [auth C] DB [auth C] AA [auth A], BA [auth A], CA [auth A], CB [auth C], DB [auth C], EB [auth D], F [auth A], FA [auth A], FB [auth D], G [auth A], GB [auth D], HA [auth A], IA [auth A], JA [auth A], JB [auth D], K [auth A], KA [auth A], LA [auth A], M [auth A], N [auth A], NA [auth A], O [auth A], P [auth A], PA [auth A], Q [auth A], R [auth A], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], WA [auth B], XA [auth B], ZA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth D] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth D] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.185
R-Value Work: 0.150
R-Value Observed: 0.152
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.43	α = 90
b = 86.43	β = 90
c = 246.12	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-22

Deposition Author(s):

Boniecki, M.T.

Cygler, M.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2020-04-22
Type: Initial release
Version 1.1: 2023-10-18
Changes: Advisory, Data collection, Database references, Refinement description