6RFR

Cryo-EM structure of respiratory complex I from Yarrowia lipolytica at 3.2 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease.

Parey, K.Haapanen, O.Sharma, V.Kofeler, H.Zullig, T.Prinz, S.Siegmund, K.Wittig, I.Mills, D.J.Vonck, J.Kuhlbrandt, W.Zickermann, V.

(2019) Sci Adv 5: eaax9484-eaax9484

  • DOI: 10.1126/sciadv.aax9484
  • Primary Citation of Related Structures:  
    6RFQ, 6RFR, 6RFS

  • PubMed Abstract: 
  • Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is associated with severe human diseases. Assembly of the one-megadalton complex I in the inner mitochondrial membrane requires assembly factors and chaperones ...

    Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is associated with severe human diseases. Assembly of the one-megadalton complex I in the inner mitochondrial membrane requires assembly factors and chaperones. We have determined the structure of complex I from the aerobic yeast Yarrowia lipolytica by electron cryo-microscopy at 3.2-Å resolution. A ubiquinone molecule was identified in the access path to the active site. The electron cryo-microscopy structure indicated an unusual lipid-protein arrangement at the junction of membrane and matrix arms that was confirmed by molecular simulations. The structure of a complex I mutant and an assembly intermediate provide detailed molecular insights into the cause of a hereditary complex I-linked disease and complex I assembly in the inner mitochondrial membrane.


    Organizational Affiliation

    Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)A728Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)B488Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)C466Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)D87Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)E375Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)F144Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)G281Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)H243Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)I229Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)J198Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)K210Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)L89Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)M136Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)N [auth O]109Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)O [auth P]124Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)P [auth Q]132Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)Q [auth R]109Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)R [auth S]249Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)S [auth U]172Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)T [auth W]123Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)U [auth X]169Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)V [auth Y]161Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)W [auth Z]182Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)X [auth a]149Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)Y [auth b]74Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_E00527g
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)Z [auth c]60Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)AA [auth d]92Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)BA [auth e]67Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_129560YALI1_D30003g
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)CA [auth f]87Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)DA [auth g]78Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)EA [auth h]138Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)FA [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: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)GA [auth j]93Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)HA [auth n]120Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)IA [auth 1]341Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)JA [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: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)KA [auth 3]128Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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UniProt GroupQ9B6C7
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)LA [auth 4]486Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for Q9B6D6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)MA [auth 5]655Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for Q9B6D3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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UniProt GroupQ9B6D3
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)NA [auth 6]185Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6E9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)OA [auth 8]99Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for B5FVG1 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)PA [auth 9]89Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for B5RSL7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
GC [auth 4],
OB [auth X],
PB [auth Z],
RB [auth g],
UB [auth j],
GC [auth 4],
OB [auth X],
PB [auth Z],
RB [auth g],
UB [auth j],
YA [auth E]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
LMN
Query on LMN

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DB [auth J],
TB [auth j]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
 Ligand Interaction
T7X
Query on T7X

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AC [auth 2],
CC [auth 2],
DC [auth 3],
JC [auth 5]
Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
 Ligand Interaction
UQ9
Query on UQ9

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WB [auth 1]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
 Ligand Interaction
CPL
Query on CPL

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BC [auth 2]1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N
 Ligand Interaction
3PE
Query on 3PE

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CB [auth J],
EB [auth J],
EC [auth 4],
FC [auth 4],
HC [auth 4],
CB [auth J],
EB [auth J],
EC [auth 4],
FC [auth 4],
HC [auth 4],
IC [auth 4],
KC [auth 5],
MC [auth 5],
NB [auth W],
QB [auth b],
SB [auth g],
VA [auth C],
XA [auth E],
YB [auth 1],
ZB [auth 1]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
NDP
Query on NDP

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WA [auth E]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
PLC
Query on PLC

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GB [auth K],
KB [auth W],
LB [auth W],
LC [auth 5],
MB [auth W],
GB [auth K],
KB [auth W],
LB [auth W],
LC [auth 5],
MB [auth W],
VB [auth n],
XB [auth 1]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
 Ligand Interaction
ZMP
Query on ZMP

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IB [auth O],
JB [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
 Ligand Interaction
FMN
Query on FMN

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UA [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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AB [auth I],
BB [auth I],
FB [auth K],
QA [auth A],
RA [auth A],
AB [auth I],
BB [auth I],
FB [auth K],
QA [auth A],
RA [auth A],
TA [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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SA [auth A],
ZA [auth H]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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HB [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyZI 552/4-2

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Refinement description
  • Version 1.2: 2019-12-25
    Changes: Database references
  • Version 1.3: 2021-06-02
    Changes: Derived calculations, Structure summary