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- PDB-5xtb: Cryo-EM structure of human respiratory complex I matrix arm -

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Entry
Database: PDB / ID: 5xtb
TitleCryo-EM structure of human respiratory complex I matrix arm
DescriptorAcyl carrier protein,mitochondrial
NADH-ubiquinone oxidoreductase 75 kDa subunit,mitochondrial
(NADH dehydrogenase [ubiquinone] flavoprotein ...) x 3
(NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 6
(NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 7
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / Respiratory / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Specimen sourceHomo sapiens / human
MethodElectron microscopy (3.4 Å resolution / Particle / Single particle)
AuthorsGu, J. / Wu, M. / Yang, M.
CitationCell, 2017, 170, 1247-1257.e12

Cell, 2017, 170, 1247-1257.e12 StrPapers
Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2.
Runyu Guo / Shuai Zong / Meng Wu / Jinke Gu / Maojun Yang

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 18, 2017 / Release: Aug 30, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 30, 2017Structure modelrepositoryInitial release
1.1Sep 6, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Assembly

Deposited unit
A: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
E: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
F: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
G: Acyl carrier protein, mitochondrial
H: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
I: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
J: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
K: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
L: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
M: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
N: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
O: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
P: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
T: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,62229
Polyers397,41818
Non-polymers4,20411
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)87770
ΔGint (kcal/M)-505
Surface area (Å2)125730

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Components

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules AKO

#1: Polypeptide(L)NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-51kD / CI-51kD / NADH dehydrogenase flavoprotein 1 / NADH-ubiquinone oxidoreductase 51 kDa subunit


Mass: 47323.938 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-457 / Source: (natural) Homo sapiens / References: UniProt: P49821, EC: 1.6.5.3, EC: 1.6.99.3
#10: Polypeptide(L)NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Complex I-9kD / CI-9kD / NADH-ubiquinone oxidoreductase 9 kDa subunit / Renal carcinoma antigen NY-REN-4


Mass: 3900.312 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 74-106 / Source: (natural) Homo sapiens / References: UniProt: P56181
#14: Polypeptide(L)NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 24 kDa subunit


Mass: 23430.881 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 36-247 / Source: (natural) Homo sapiens / References: UniProt: P19404, EC: 1.6.5.3, EC: 1.6.99.3

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 6 types, 6 molecules BCLPQT

#2: Polypeptide(L)NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Complex I-23kD / CI-23kD / NADH-ubiquinone oxidoreductase 23 kDa subunit / TYKY subunit


Mass: 20314.037 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: O00217, EC: 1.6.5.3, EC: 1.6.99.3
#3: Polypeptide(L)NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Complex I-20kD / CI-20kD / NADH-ubiquinone oxidoreductase 20 kDa subunit / PSST subunit


Mass: 17887.928 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 58-213 / Source: (natural) Homo sapiens / References: UniProt: O75251, EC: 1.6.5.3, EC: 1.6.99.3
#11: Polypeptide(L)NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / CI-18 kDa / Complex I-AQDQ / CI-AQDQ / NADH-ubiquinone oxidoreductase 18 kDa subunit


Mass: 13721.598 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 58-175 / Source: (natural) Homo sapiens / References: UniProt: O43181
#15: Polypeptide(L)NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Complex I-30kD / CI-30kD / NADH-ubiquinone oxidoreductase 30 kDa subunit


Mass: 24432.656 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 43-250 / Source: (natural) Homo sapiens / References: UniProt: O75489, EC: 1.6.5.3, EC: 1.6.99.3
#16: Polypeptide(L)NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / CI-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 43987.625 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 79-463 / Source: (natural) Homo sapiens / References: UniProt: O75306, EC: 1.6.5.3, EC: 1.6.99.3
#17: Polypeptide(L)NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Complex I-13kD-A / CI-13kD-A / NADH-ubiquinone oxidoreductase 13 kDa-A subunit


Mass: 10578.848 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: O75380

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 7 types, 7 molecules EFHIJNW

#4: Polypeptide(L)NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / CI-B14 / LYR motif-containing protein 6 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 13758.070 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-154 / Source: (natural) Homo sapiens / References: UniProt: P56556
#5: Polypeptide(L)NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Complex I-B8 / CI-B8 / NADH-ubiquinone oxidoreductase B8 subunit


Mass: 9535.905 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 14-96 / Source: (natural) Homo sapiens / References: UniProt: O43678
#7: Polypeptide(L)NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Complex I subunit B13 / Complex I-13kD-B / CI-13kD-B / NADH-ubiquinone oxidoreductase 13 kDa-B subunit


Mass: 13119.208 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: Q16718
#8: Polypeptide(L)NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Complex I-B14.5a / CI-B14.5a / NADH-ubiquinone oxidoreductase subunit B14.5a


Mass: 12282.051 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 4-113 / Source: (natural) Homo sapiens / References: UniProt: O95182
#9: Polypeptide(L)NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / CI-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 38387.594 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 40-375 / Source: (natural) Homo sapiens / References: UniProt: Q16795
#13: Polypeptide(L)NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / 13 kDa differentiation-associated protein / Complex I-B17.2 / CIB17.2 / NADH-ubiquinone oxidoreductase subunit B17.2


Mass: 16880.068 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: Q9UI09
#18: Polypeptide(L)NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic and interferon-induced mortality 19 protein / Gene associated with retinoic and IFN-induced mortality 19 protein / NADH-ubiquinone oxidoreductase B16.6 subunit


Mass: 2560.952 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 7-28 / Source: (natural) Homo sapiens / References: UniProt: Q9P0J0

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Polypeptide(L) , 2 types, 2 molecules GM

#6: Polypeptide(L)Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 9845.247 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: O14561
#12: Polypeptide(L)NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Complex I-75kD / CI-75kD


Mass: 75471.484 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 30-716 / Source: (natural) Homo sapiens / References: UniProt: P28331, EC: 1.6.5.3, EC: 1.6.99.3

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Non-polymers , 5 types, 11 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Formula: Fe4S4
#20: ChemicalChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Formula: C17H21N4O9P
#21: ChemicalChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Formula: C23H45N2O8PS
#22: ChemicalChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Formula: C21H30N7O17P3
#23: 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: Human respiratory complex I matrix arm / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1EMAN2.1PARTICLE SELECTION1
2AutoEMation2.0IMAGE ACQUISITION1
4CTFFIND3.0CTF CORRECTION1
7COOT0.8.2MODEL FITTING1
9RELION1.4INITIAL EULER ASSIGNMENT1
10RELION1.4FINAL EULER ASSIGNMENT1
11RELION1.4CLASSIFICATION1
12RELION1.4RECONSTRUCTION1
13PHENIX1.11.1MODEL REFINEMENT1
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 167761 / Symmetry type: POINT

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