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- PDB-6kls: Hyperthermophilic respiratory Complex III -

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Basic information

Entry
Database: PDB / ID: 6kls
TitleHyperthermophilic respiratory Complex III
Components
  • Cytochrome c
  • Rieske-I iron sulfur protein
  • cytochrome b subunit
KeywordsOXIDOREDUCTASE / Respiratory chain / Complex III / Hyperthermophilic mechanism
Function / homology
Function and homology information


ubiquinol-cytochrome-c reductase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome b(N-terminal)/b6/petB / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal ...Cytochrome b(N-terminal)/b6/petB / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Cytochrome c / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DLX / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-PGV / Cytochrome c / Cytochrome b / Rieske-I iron sulfur protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFei, S. / Hartmut, M. / Yun, Z. / Guohong, P. / Guoliang, Z. / Hui, Z. / Shuangbo, Z. / Xiaoyun, P. / Yan, Z.
CitationJournal: Angew Chem Int Ed Engl / Year: 2020
Title: A 3.3 Å-Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability.
Authors: Guoliang Zhu / Hui Zeng / Shuangbo Zhang / Jana Juli / Xiaoyun Pang / Jan Hoffmann / Yan Zhang / Nina Morgner / Yun Zhu / Guohong Peng / Hartmut Michel / Fei Sun /
Abstract: Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc complex (Complex III) from ...Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Å resolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N-terminus of cyt. c was found to greatly enhance the interaction between cyt. b and cyt. c , and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc complex in an extreme thermal environment.
History
DepositionJul 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 2.0Apr 7, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / em_software ...atom_site / em_software / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.category / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Description: Ligand geometry / Provider: author / Type: Coordinate replacement

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Rieske-I iron sulfur protein
B: cytochrome b subunit
C: Cytochrome c
D: Rieske-I iron sulfur protein
E: cytochrome b subunit
F: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,44723
Polymers188,3116
Non-polymers10,13617
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area38500 Å2
ΔGint-418 kcal/mol
Surface area64360 Å2

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Rieske-I iron sulfur protein


Mass: 19429.857 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5 / References: UniProt: O66460
#2: Protein cytochrome b subunit


Mass: 47045.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (bacteria) / References: UniProt: O66459*PLUS
#3: Protein Cytochrome c


Mass: 27680.170 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5 / References: UniProt: O66458

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Non-polymers , 5 types, 17 molecules

#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-DLX / 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione


Mass: 639.004 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C45H66O2
#7: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#8: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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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: The cytochrome bc1 complex (respiratory complex III) / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Aquifex aeolicus (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93622 / Symmetry type: POINT

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