7B0N

A 3.7-angstrom structure of Yarrowia lipolytica complex I with an R121M mutation in NUCM.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

A conserved arginine residue is critical for stabilizing the N2 FeS cluster in mitochondrial complex I.

Hameedi, M.A.Grba, D.N.Richardson, K.H.Jones, A.J.Y.Song, W.Roessler, M.M.Wright, J.J.Hirst, J.

(2021) J Biol Chem 296: 100474-100474

  • DOI: https://doi.org/10.1016/j.jbc.2021.100474
  • Primary Citation of Related Structures:  
    7B0N

  • PubMed Abstract: 

    Respiratory complex I (NADH:ubiquinone oxidoreductase), the first enzyme of the electron-transport chain, captures the free energy released by NADH oxidation and ubiquinone reduction to translocate protons across an energy-transducing membrane and drive ATP synthesis during oxidative phosphorylation. The cofactor that transfers the electrons directly to ubiquinone is an iron-sulfur cluster (N2) located in the NDUFS2/NUCM subunit. A nearby arginine residue (R121), which forms part of the second coordination sphere of the N2 cluster, is known to be posttranslationally dimethylated but its functional and structural significance are not known. Here, we show that mutations of this arginine residue (R121M/K) abolish the quinone-reductase activity, concomitant with disappearance of the N2 signature from the electron paramagnetic resonance (EPR) spectrum. Analysis of the cryo-EM structure of NDUFS2-R121M complex I at 3.7 Å resolution identified the absence of the cubane N2 cluster as the cause of the dysfunction, within an otherwise intact enzyme. The mutation further induced localized disorder in nearby elements of the quinone-binding site, consistent with the close connections between the cluster and substrate-binding regions. Our results demonstrate that R121 is required for the formation and/or stability of the N2 cluster and highlight the importance of structural analyses for mechanistic interpretation of biochemical and spectroscopic data on complex I variants.


  • Organizational Affiliation

    Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3128Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad3YALI1_M00472r
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for S5TMS4 (Yarrowia lipolytica)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)210Yarrowia lipolyticaMutation(s): 0 
Gene Names: nukmYALI1_F09003g
EC: 1.6.99.3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NUGM protein293Yarrowia lipolyticaMutation(s): 0 
Gene Names: nugmB0I71DRAFT_126141
EC: 1.6.99.3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NUCM protein466Yarrowia lipolyticaMutation(s): 1 
Gene Names: nucmB0I71DRAFT_131656YALI1_F22993g
EC: 1.6.99.3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)243Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuhm
EC: 1.6.99.3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)488Yarrowia lipolyticaMutation(s): 0 
Gene Names: nubmNUO51YALI1_B26679g
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)728Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuamYALI1_D07089g
EC: 1.6.99.3
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1341Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad1YALI1_M00064g
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I)193Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuimB0I71DRAFT_132693YALI1_F01456g
EC: 1.6.99.3
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6185Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad6YALI1_M00056g
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4L89Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad4LYALI1_M00335g
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5655Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad5YALI1_M00338r
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for S5TF58 (Yarrowia lipolytica)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4486Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad4YALI1_M00296g
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2469Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad2YALI1_M00458g
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)169Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_E33570g
Membrane Entity: Yes 
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Find proteins for A0A1D8NKB4 (Yarrowia lipolytica)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Epimerase domain-containing protein355Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_137087
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Find proteins for A0A371BY45 (Yarrowia lipolytica)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)161Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_B19507g
Membrane Entity: Yes 
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Find proteins for A0A1D8N7X0 (Yarrowia lipolytica)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
zf-CHCC domain-containing protein118Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_130567YALI1_D24109g
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Find proteins for A0A1H6Q8Z5 (Yarrowia lipolytica)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)87Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_C04281g
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein81Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_165126YALI1_D18037g
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein88Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_D32594g
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)144Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_119420BD777DRAFT_112063
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)124Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_A01824g
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)172Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_134276
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B14.7180Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_129038
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
GRIM-19122Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_132113YALI1_E34222g
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1AA [auth a]86Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_173710YALI1_C30086g
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)BA [auth b]78Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_131413YALI1_E28107g
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)CA [auth c]182Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_129288YALI1_A03153g
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
subunit NEBM of protein NADH:Ubiquinone Oxidoreductase (Complex I) [Yarrowia lipolytica]DA [auth d]73Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_E00527g
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)EA [auth e]89Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_F24343g
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)FA [auth f]138Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_100046YALI1_B00908g
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)GA [auth g]249Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuwmB0I71DRAFT_98177YALI1_E34367g
EC: 1.6.99.3
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Find proteins for Q6ZY23 (Yarrowia lipolytica)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
subunit NUNM of protein NADH:Ubiquinone Oxidoreductase (Complex I)HA [auth h]139Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_126580
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)IA [auth i]90Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_133979YALI1_D22691g
Membrane Entity: Yes 
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Find proteins for A0A1H6Q311 (Yarrowia lipolytica)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)JA [auth j]67Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_129560YALI1_D30003g
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UniProt GroupA0A1D8NFX6
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)KA [auth k]60Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_135324
Membrane Entity: Yes 
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Find proteins for A0A371C0F2 (Yarrowia lipolytica)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)LA [auth l]149Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_129122YALI1_D06302g
Membrane Entity: Yes 
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Find proteins for A0A1D8ND94 (Yarrowia lipolytica)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)MA [auth m]93Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuvmYALI1_F09017g
EC: 1.6.99.3
Membrane Entity: Yes 
UniProt
Find proteins for Q6ZY24 (Yarrowia lipolytica)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)NA [auth n]109Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_D09203g
Membrane Entity: Yes 
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Find proteins for A0A1D8NDL1 (Yarrowia lipolytica)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)OA [auth o]99Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_E37603g
Membrane Entity: Yes 
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Find proteins for A0A1H6PKH9 (Yarrowia lipolytica)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)PA [auth p]92Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_A18188g
Membrane Entity: Yes 
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Find proteins for A0A1D8N596 (Yarrowia lipolytica)
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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IB [auth M],
MB [auth O],
UB [auth Z],
WB [auth a],
XB [auth b]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
3PE
Query on 3PE

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AB [auth I]
AC [auth d]
BC [auth g]
FB [auth L]
GB [auth L]
AB [auth I],
AC [auth d],
BC [auth g],
FB [auth L],
GB [auth L],
HB [auth L],
JB [auth M],
LB [auth N],
TB [auth Y],
VB [auth Z],
XA [auth H],
YB [auth b],
ZA [auth H]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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NB [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PLC
Query on PLC

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DB [auth L]
EB [auth L]
KB [auth N]
QA [auth D]
YA [auth H]
DB [auth L],
EB [auth L],
KB [auth N],
QA [auth D],
YA [auth H],
ZB [auth d]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
EHZ
Query on EHZ

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PB [auth T],
QB [auth U]
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
C25 H49 N2 O9 P S
JYSKQPQRUCZFIQ-REWPJTCUSA-N
LMT
Query on LMT

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RB [auth Y],
SB [auth Y]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FMN
Query on FMN

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SA [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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BB [auth I],
CB [auth I],
TA [auth F],
UA [auth G],
VA [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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RA [auth E],
WA [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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OB [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.16

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105663141
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/2

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 2.0: 2021-06-02
    Changes: Atomic model
  • Version 2.1: 2021-07-21
    Changes: Database references, Derived calculations, Structure summary
  • Version 3.0: 2022-12-07
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary