6WI2 | pdb_00006wi2

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 (Depositor), 0.190 (DCC)
R-Value Work:
0.150 (Depositor), 0.160 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
View more details

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 LOADING

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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 LOADING

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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 LOADING

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 LOADING

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 GA [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain OA [auth A] SDF format, chain QA [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 EA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain QA [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 EA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain QA [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 EA [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 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 GB [auth D] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [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 WA [auth B] SDF format, chain XA [auth B] SDF format, chain ZA [auth B] SDF format, chain CB [auth C] SDF format, chain V [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] 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 GB [auth D] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [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 WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain V [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] 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 GB [auth D] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [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 WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain V [auth A]	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 (Depositor), 0.190 (DCC)
R-Value Work: 0.150 (Depositor), 0.160 (DCC)
R-Value Observed: 0.152 (Depositor)

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