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- PDB-7z7t: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Op... -

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Basic information

Entry
Database: PDB / ID: 7z7t
TitleComplex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state
Components
  • (NADH dehydrogenase I subunit ...) x 2
  • (NADH-quinone oxidoreductase subunit ...) x 9
  • NADH dehydrogenase subunit L
  • NADH-quinone oxidoreductase
KeywordsPROTON TRANSPORT / Complex I / NADH / Quinone
Function / homology
Function and homology information


NADH dehydrogenase (quinone) / : / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase complex / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / NADH dehydrogenase activity ...NADH dehydrogenase (quinone) / : / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase complex / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / NADH dehydrogenase activity / respiratory chain complex I / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
NADH dehydrogenase, subunit CD / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / : ...NADH dehydrogenase, subunit CD / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / : / NADH-quinone oxidoreductase, subunit D / Aspartate decarboxylase-like domain superfamily / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Thioredoxin-like [2Fe-2S] ferredoxin / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / EICOSANE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit L / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase ...1,2-Distearoyl-sn-glycerophosphoethanolamine / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / EICOSANE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit L / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit B
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MC4100 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKravchuk, V. / Kampjut, D. / Sazanov, L.
Funding support Austria, 1items
OrganizationGrant numberCountry
Not funded25541 Austria
CitationJournal: Nature / Year: 2022
Title: A universal coupling mechanism of respiratory complex I.
Authors: Vladyslav Kravchuk / Olga Petrova / Domen Kampjut / Anna Wojciechowska-Bason / Zara Breese / Leonid Sazanov /
Abstract: Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone ...Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a 'domino effect' series of proton transfers and electrostatic interactions: the forward wave ('dominoes stacking') primes the pump, and the reverse wave ('dominoes falling') results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes.
History
DepositionMar 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: NADH-quinone oxidoreductase subunit F
E: NADH dehydrogenase I subunit E
G: NADH-quinone oxidoreductase
C: NADH-quinone oxidoreductase subunit C/D
B: NADH-quinone oxidoreductase subunit B
I: NADH-quinone oxidoreductase subunit I
J: NADH-quinone oxidoreductase subunit J
H: NADH-quinone oxidoreductase subunit H
A: NADH-quinone oxidoreductase subunit A
L: NADH dehydrogenase subunit L
M: NADH dehydrogenase I subunit M
N: NADH-quinone oxidoreductase subunit N
K: NADH-quinone oxidoreductase subunit K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)551,73336
Polymers540,92613
Non-polymers10,80723
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NADH-quinone oxidoreductase subunit ... , 9 types, 9 molecules FCBIJHANK

#1: Protein NADH-quinone oxidoreductase subunit F


Mass: 49352.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: A0A037YNA7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#4: Protein NADH-quinone oxidoreductase subunit C/D / NADH dehydrogenase I subunit C/D / NDH-1 subunit C/D


Mass: 68321.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: A0A024L1E0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#5: Protein NADH-quinone oxidoreductase subunit B / NADH dehydrogenase I subunit B / NDH-1 subunit B


Mass: 25081.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: V0ZV11, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein NADH-quinone oxidoreductase subunit I


Mass: 20562.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: A0A1X3LLK1
#7: Protein NADH-quinone oxidoreductase subunit J


Mass: 19889.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: A0A0H3MIP2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#8: Protein NADH-quinone oxidoreductase subunit H / NADH dehydrogenase I subunit H / NDH-1 subunit H


Mass: 36240.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: E6BKM7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#9: Protein NADH-quinone oxidoreductase subunit A / NADH dehydrogenase I subunit A / NDH-1 subunit A / NUO1


Mass: 16474.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: A0A862ZI24, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#12: Protein NADH-quinone oxidoreductase subunit N / NADH dehydrogenase I subunit N / NDH-1 subunit N


Mass: 52072.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: E2QPD7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#13: Protein NADH-quinone oxidoreductase subunit K / NADH dehydrogenase I subunit K / NDH-1 subunit K


Mass: 10852.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: A0A7U9LRT0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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NADH dehydrogenase I subunit ... , 2 types, 2 molecules EM

#2: Protein NADH dehydrogenase I subunit E / NADH-quinone oxidoreductase subunit E / NDH-1 subunit E


Mass: 18614.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: A0A829CRH1
#11: Protein NADH dehydrogenase I subunit M / NADH-quinone oxidoreductase subunit M / NDH-1 subunit M


Mass: 56560.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: C3T2G7

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Protein , 2 types, 2 molecules GL

#3: Protein NADH-quinone oxidoreductase


Mass: 100419.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: A0A037YPU0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#10: Protein NADH dehydrogenase subunit L / NADH-quinone oxidoreductase subunit L / NADH:ubiquinone oxidoreductase subunit L / NADH:ubiquinone ...NADH-quinone oxidoreductase subunit L / NADH:ubiquinone oxidoreductase subunit L / NADH:ubiquinone oxidoreductase / membrane subunit L


Mass: 66483.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MC4100 (bacteria)
References: UniProt: A0A024L0E1, NADH dehydrogenase (quinone), NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 7 types, 23 molecules

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


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4
#15: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#16: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#17: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#18: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#19: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#20: Chemical ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H42

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex I / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Escherichia coli str. K-12 substr. MC4100 (bacteria)
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMESC6H13NO4S1
22 mMcalcium chlorideCaCl21
3250 mMsodium chlorideNaCl1
40.01 %LMNGC47H88O221
50.25 mg/mlE. coli lipid extractC40H80NO8P1
60.1 %CHAPSC32H58N2O7S1
72 mMNADHC21H27N7O14P21
80.8 mMDQC19H30O41
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11316
Image scansSampling size: 5 µm

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refinedev_4092+SVNrefinement
PHENIXdev_4092+SVNrefinement
EM software
IDNameCategory
1RELIONparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4483166
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31887 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: ML
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14HEA

4hea

14HEA1PDBexperimental model
23RKO

3rko

13RKO2PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 42.53 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004838331
ELECTRON MICROSCOPYf_angle_d0.739752003
ELECTRON MICROSCOPYf_chiral_restr0.04625807
ELECTRON MICROSCOPYf_plane_restr0.00636518
ELECTRON MICROSCOPYf_dihedral_angle_d12.30185602

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