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- PDB-4uq8: Electron cryo-microscopy of bovine Complex I -

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Entry
Database: PDB / ID: 4uq8
TitleElectron cryo-microscopy of bovine Complex I
DescriptorNADH-UBIQUINONE OXIDOREDUCTASE 75 KDA SUBUNIT,MITOCHONDRIAL
ACYL CARRIER PROTEIN,MITOCHONDRIAL
NADH UBIQUINONE DEHYDROGENASE
(NADH UBIQUINONE OXIDOREDUCTASE CHAIN ...) x 6
(NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN ...) x 4
and more 4 items
KeywordsOXIDOREDUCTASE / NADH DEHYDROGENASE / RESPIRATORY COMPLEX
Specimen sourceBos taurus / mammal / CATTLE / ウシ /
MethodElectron microscopy (4.95 Å resolution / Particle / Single particle)
AuthorsVinothkumar, K.R. / Zhu, J. / Hirst, J.
CitationNature, 2014, 515, 80-84

Nature, 2014, 515, 80-84 Yorodumi Papers
Architecture of mammalian respiratory complex I.
Kutti R Vinothkumar / Jiapeng Zhu / Judy Hirst

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 21, 2014 / Release: Oct 1, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 1, 2014Structure modelrepositoryInitial release
1.1Nov 12, 2014Structure modelDatabase references
1.2Aug 2, 2017Structure modelData collectionem_software_em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Assembly

Deposited unit
A: NADH UBIQUINONE OXIDOREDUCTASE CHAIN 3
B: NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 7, MITOCHONDRIAL
C: NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 3, MITOCHONDRIAL
D: NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 2, MITOCHONDRIAL
E: NADH DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN 2, MITOCHONDRIAL
F: NADH DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN 1, MITOCHONDRIAL
G: NADH-UBIQUINONE OXIDOREDUCTASE 75 KDA SUBUNIT, MITOCHONDRIAL
H: NADH UBIQUINONE OXIDOREDUCTASE CHAIN 1
I: NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 8, MITOCHONDRIAL
J: NADH UBIQUINONE OXIDOREDUCTASE CHAIN 6
K: NADH UBIQUINONE OXIDOREDUCTASE CHAIN 4L
L: NADH UBIQUINONE OXIDOREDUCTASE CHAIN 5
M: NADH UBIQUINONE OXIDOREDUCTASE CHAIN 4
N: NADH UBIQUINONE OXIDOREDUCTASE CHAIN 2
O: NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 10
P: NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 9, MITOCHONDRIAL
Q: NADH DEHYDROGENASE [UBIQUINONE] SUBUNIT 4
R: NADH DEHYDROGENASE [UBIQUINONE] SUBUNIT 6
S: NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 2
T: ACYL CARRIER PROTEIN, MITOCHONDRIAL
U: NADH UBIQUINONE DEHYDROGENASE
V: NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT; 5
W: NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT; 6
X: NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 8
Y: NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT; 11
Z: NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 13
a: NADH UBIQUINONE OXIDOREDUCTASE
b: NADH UBIQUINONE OXIDOREDUCTASE
c: NADH UBIQUINONE OXIDOREDUCTASE
d: NADH UBIQUINONE OXIDOREDUCTASE
e: NADH UBIQUINONE OXIDOREDUCTASE
f: NADH UBIQUINONE OXIDOREDUCTASE
g: NADH UBIQUINONE OXIDOREDUCTASE
h: NADH UBIQUINONE OXIDOREDUCTASE
i: NADH UBIQUINONE OXIDOREDUCTASE
j: NADH UBIQUINONE OXIDOREDUCTASE
k: NADH UBIQUINONE OXIDOREDUCTASE
l: NADH UBIQUINONE OXIDOREDUCTASE
m: NADH UBIQUINONE OXIDOREDUCTASE
n: NADH UBIQUINONE OXIDOREDUCTASE
o: NADH UBIQUINONE OXIDOREDUCTASE
p: NADH UBIQUINONE OXIDOREDUCTASE
q: NADH UBIQUINONE OXIDOREDUCTASE
r: NADH UBIQUINONE OXIDOREDUCTASE
s: NADH UBIQUINONE OXIDOREDUCTASE
t: NADH UBIQUINONE OXIDOREDUCTASE
u: NADH UBIQUINONE OXIDOREDUCTASE
v: NADH UBIQUINONE OXIDOREDUCTASE
w: NADH UBIQUINONE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)517,63557
Polyers515,17449
Non-polymers2,4618
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

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NADH UBIQUINONE ... , 25 types, 31 molecules AHJKLMNUab...

#1: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE CHAIN 3


Mass: 9464.658 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#8: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE CHAIN 1


Mass: 26655.701 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#10: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE CHAIN 6


Mass: 14570.941 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#11: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE CHAIN 4L


Mass: 7166.825 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#12: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE CHAIN 5


Mass: 51166.188 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#13: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE CHAIN 4


Mass: 38570.516 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#14: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE CHAIN 2


Mass: 29379.080 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#21: Polypeptide(L)NADH UBIQUINONE DEHYDROGENASE


Mass: 6727.274 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#27: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 2486.056 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#28: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 3592.419 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#29: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 2315.846 Da / Num. of mol.: 2 / Source: (natural) BOS TAURUS
#30: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 3337.105 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#31: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 1720.111 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#32: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 2571.161 Da / Num. of mol.: 3 / Source: (natural) BOS TAURUS
#33: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 1890.321 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#34: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 2060.531 Da / Num. of mol.: 2 / Source: (natural) BOS TAURUS
#35: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 2400.951 Da / Num. of mol.: 3 / Source: (natural) BOS TAURUS
#36: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 2911.580 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#37: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 5039.203 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#38: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 1805.216 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#39: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 2145.636 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#40: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 2230.741 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#41: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 4868.993 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#42: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 3677.524 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#43: Polypeptide(L)NADH UBIQUINONE OXIDOREDUCTASE


Mass: 2741.370 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS

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NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN ... , 4 types, 4 molecules BCDI

#2: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 7, MITOCHONDRIAL


Mass: 12260.168 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#3: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 3, MITOCHONDRIAL


Mass: 13124.170 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#4: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 2, MITOCHONDRIAL


Mass: 32698.209 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#9: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 8, MITOCHONDRIAL


Mass: 13949.309 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS

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NADH DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN ... , 2 types, 2 molecules EF

#5: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN 2, MITOCHONDRIAL


Mass: 13621.847 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#6: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN 1, MITOCHONDRIAL


Mass: 35068.211 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS

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Polypeptide(L) , 2 types, 2 molecules GT

#7: Polypeptide(L)NADH-UBIQUINONE OXIDOREDUCTASE 75 KDA SUBUNIT, MITOCHONDRIAL


Mass: 46055.980 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#20: Polypeptide(L)ACYL CARRIER PROTEIN, MITOCHONDRIAL


Mass: 6400.881 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS

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NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT ... , 5 types, 5 molecules OPSXZ

#15: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 10


Mass: 18741.035 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#16: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 9, MITOCHONDRIAL


Mass: 25804.662 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#19: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 2


Mass: 6826.406 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#24: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 8


Mass: 6741.301 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#26: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 13


Mass: 5549.833 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS

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NADH DEHYDROGENASE [UBIQUINONE] SUBUNIT ... , 2 types, 2 molecules QR

#17: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] SUBUNIT 4


Mass: 7251.930 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#18: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] SUBUNIT 6


Mass: 4017.944 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS

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NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT; ... , 3 types, 3 molecules VWY

#22: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT; 5


Mass: 6060.462 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#23: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT; 6


Mass: 6145.567 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS
#25: Polypeptide(L)NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT; 11


Mass: 9039.134 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS

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Non-polymers , 2 types, 8 molecules

#44: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Formula: Fe4S4
#45: ChemicalChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: NADH-UBIQUINONE OXIDOREDUCTASE / Type: COMPLEX / Details: ONE IMAGE PER HOLE WAS TAKEN.
Buffer solutionName: 20MM TRIS-HCL, 150 MM NACL, 0.03% CYMAL-7 / Details: 20MM TRIS-HCL, 150 MM NACL, 0.03% CYMAL-7 / pH: 8
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 100, INSTRUMENT- OTHER, METHOD- THE SPECIMEN WAS VITRIFIED IN AN ENVIRONMENTAL PLUNGE-FREEZE APPARATUS (BELLARE ET AL, J.ELECTR. MICROS. TECH., 1988, 10, 87-111). BLOT FOR 15- 18 SECONDS AFTER THE DIAMETER OF THE BLOTTED MENISCUS CEASES TO EXPAND AND PLUNGED.,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Oct 21, 2013
Details: EACH IMAGE WAS EXPOSED FOR 4 SECONDS RESULTING IN A TOTAL DOSE OF ABOUT 64 ELECTRONS.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 / Calibrated magnification: 81495 / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Specimen holderTemperature: 85 kelvins
Image recordingElectron dose: 64 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNumber digital images: 1154
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
1UCSF ChimeraMODEL FITTING1
2RELIONRECONSTRUCTION1
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1
3D reconstructionMethod: RELION / Resolution: 4.95 Å / Number of particles: 25492 / Actual pixel size: 1.717
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2676(DEPOSITION ID: 12566).AUTHORS HAVE USED COOT TO FIX SOME CLOSE CONTACTS AND RESET THE B-FACTOR. AS THIS MODEL IS NOT REFINED, HENCE THE B-FACTOR DOES NOT MEAN ANYTHING.
Symmetry type: POINT
Atomic model buildingRef space: REAL
Least-squares processHighest resolution: 4.95 Å
Refine hist #LASTHighest resolution: 4.95 Å
Number of atoms included #LASTProtein: 28591 / Nucleic acid: 0 / Ligand: 56 / Solvent: 0 / Total: 28647

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