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 7O6Y | pdb_00007o6y

Cryo-EM structure of respiratory complex I under turnover


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history. 

Literature

High-resolution structure and dynamics of mitochondrial complex I-Insights into the proton pumping mechanism.

Parey, K., Lasham, J., Mills, D.J., Djurabekova, A., Haapanen, O., Yoga, E.G., Xie, H., Kuhlbrandt, W., Sharma, V., Vonck, J., Zickermann, V.

(2021) Sci Adv 7: eabj3221-eabj3221

  • DOI: https://doi.org/10.1126/sciadv.abj3221
  • Primary Citation Related Structures: 
    7O6Y, 7O71

  • PubMed Abstract: 

    Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1-MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined, but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from Yarrowia lipolytica at 2.1-Å resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which ~100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4-Å resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamic simulations, we define details of the proton translocation pathways and offer insights into the redox-coupled proton pumping mechanism of complex I.


  • Organizational Affiliation: 
    • Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany.

Macromolecule Content 

  • Total Structure Weight: 1,017.33 kDa 
  • Atom Count: 64,866 
  • Modeled Residue Count: 7,927 
  • Deposited Residue Count: 8,723 
  • Unique protein chains: 42

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)728Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
Find proteins for F2Z6F1 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial488Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NUCM protein466Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)D [auth G]281Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)E [auth H]243Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)F [auth I]229Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)G [auth K]210Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
Find proteins for Q6C2Q1 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LH [auth L]89Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)I [auth S]249Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)J [auth j]93Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1K [auth 1]341Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2L [auth 2]469Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3M [auth 3]128Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)N [auth 4]486Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)O [auth 5]655Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6P [auth 6]185Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)Q [auth g]78Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)R [auth D]87Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)S [auth E]375Yarrowia lipolyticaMutation(s): 0 
UniProt
Find proteins for Q6C7X4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)T [auth F]144Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q6C4W9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)U [auth J]198Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)V [auth M]136Yarrowia lipolyticaMutation(s): 0 
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Find proteins for Q6C8J9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)W [auth O]109Yarrowia lipolyticaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)X [auth P]124Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)Y [auth Q]132Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)Z [auth R]109Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)AA [auth U]172Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)BA [auth W]123Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)CA [auth X]169Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)DA [auth Y]161Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)EA [auth Z]182Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)FA [auth a]149Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)GA [auth b]74Yarrowia lipolyticaMutation(s): 0 
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Find proteins for A0A1D8NGI5 (Yarrowia lipolytica)
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)HA [auth c]60Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)IA [auth d]92Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)JA [auth e]67Yarrowia lipolyticaMutation(s): 0 
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Find proteins for A0A1D8NFX6 (Yarrowia lipolytica)
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)KA [auth f]87Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)LA [auth h]138Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)MA [auth i]90Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Go to UniProtKB:  A0A1H6Q311
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UniProt GroupA0A1H6Q311
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)NA [auth n]139Yarrowia lipolyticaMutation(s): 0 
UniProt
Find proteins for Q6C1R9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C1R9 
Go to UniProtKB:  Q6C1R9
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UniProt GroupQ6C1R9
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Reference Sequence
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)OA [auth 8]99Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B5FVG1 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore B5FVG1 
Go to UniProtKB:  B5FVG1
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UniProt GroupB5FVG1
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Reference Sequence
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)PA [auth 9]89Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B5RSL7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore B5RSL7 
Go to UniProtKB:  B5RSL7
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UniProt GroupB5RSL7
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Reference Sequence

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
FC [auth W]
GC [auth X]
HC [auth Z]
MC [auth n]
UB [auth g]
FC [auth W],
GC [auth X],
HC [auth Z],
MC [auth n],
UB [auth g],
YB [auth E]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
LMN

Query on LMN



Download:Ideal Coordinates CCD File
AC [auth J],
IC [auth a]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
T7X

Query on T7X



Download:Ideal Coordinates CCD File
IB [auth 2],
JC [auth b],
KB [auth 3]
Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
UQ9

Query on UQ9



Download:Ideal Coordinates CCD File
WA [auth C]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
CPL

Query on CPL



Download:Ideal Coordinates CCD File
HB [auth 2]1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
EB [auth 1]
FB [auth 1]
JB [auth 2]
KC [auth b]
LB [auth 4]
EB [auth 1],
FB [auth 1],
JB [auth 2],
KC [auth b],
LB [auth 4],
MB [auth 4],
NB [auth 4],
PB [auth 5],
QB [auth 5],
RB [auth 5],
SB [auth 6],
TB [auth 6],
VB [auth g],
XB [auth E],
YA [auth I],
ZB [auth J]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP

Query on NDP



Download:Ideal Coordinates CCD File
WB [auth E]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
NAI

Query on NAI



Download:Ideal Coordinates CCD File
VA [auth B]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
PLC

Query on PLC



Download:Ideal Coordinates CCD File
CB [auth K]
DB [auth 1]
EC [auth W]
GB [auth 1]
LC [auth i]
CB [auth K],
DB [auth 1],
EC [auth W],
GB [auth 1],
LC [auth i],
OB [auth 4]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
ZMP

Query on ZMP



Download:Ideal Coordinates CCD File
CC [auth O],
DC [auth Q]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
FMN

Query on FMN



Download:Ideal Coordinates CCD File
UA [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
AB [auth I]
BB [auth K]
QA [auth A]
RA [auth A]
TA [auth B]
AB [auth I],
BB [auth K],
QA [auth A],
RA [auth A],
TA [auth B],
ZA [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
SA [auth A],
XA [auth H]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
BC [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
C
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
FME
Query on FME
H [auth L]L-PEPTIDE LINKINGC6 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyZI 552/4-2

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 2.0: 2025-10-01
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2026-09-02
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary