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- PDB-8xkv: Cryo-EM structure of the Ycf2-FtsHi motor complex from Arabidopsi... -

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Basic information

Entry
Database: PDB / ID: 8xkv
TitleCryo-EM structure of the Ycf2-FtsHi motor complex from Arabidopsis in Apo state
Components
  • (Probable inactive ATP-dependent zinc metalloprotease FTSHI ...) x 4
  • (UNK) x 5
  • ATP-dependent zinc metalloprotease FTSH 12, chloroplastic
  • Aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit B
  • At4g28210
  • AtTam46
  • Embryo defective 2737
  • Malate dehydrogenase, chloroplastic
  • Protein Ycf2
KeywordsMEMBRANE PROTEIN / ATP-motor / Ycf2 / FtsHi
Function / homology
Function and homology information


regulation of photorespiration / chloroplast protein-transporting ATPase activity / Ycf2/FtsHi complex / plastid stroma / plastid fission / protein import into chloroplast stroma / chloroplast fission / stromule / chloroplast inner membrane / chloroplast membrane ...regulation of photorespiration / chloroplast protein-transporting ATPase activity / Ycf2/FtsHi complex / plastid stroma / plastid fission / protein import into chloroplast stroma / chloroplast fission / stromule / chloroplast inner membrane / chloroplast membrane / chloroplast organization / malate dehydrogenase / embryo development ending in seed dormancy / L-malate dehydrogenase (NAD+) activity / malate metabolic process / apoplast / chloroplast envelope / plasmodesma / plant-type vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / plastid / chloroplast stroma / ATP-dependent peptidase activity / chloroplast thylakoid membrane / tricarboxylic acid cycle / cell redox homeostasis / response to cold / chloroplast / metalloendopeptidase activity / defense response to bacterium / ATP hydrolysis activity / mitochondrion / proteolysis / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Uncharacterised protein family Ycf2 / Ycf2 family / : / Malate dehydrogenase, type 1 / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / Lactate/malate dehydrogenase, N-terminal ...Uncharacterised protein family Ycf2 / Ycf2 family / : / Malate dehydrogenase, type 1 / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / NAD(P)-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / Probable inactive ATP-dependent zinc metalloprotease FTSHI 2, chloroplastic / Probable inactive ATP-dependent zinc metalloprotease FTSHI 5, chloroplastic / Embryo defective 2737 / Probable inactive ATP-dependent zinc metalloprotease FTSHI 4, chloroplastic / Probable inactive ATP-dependent zinc metalloprotease FTSHI 1, chloroplastic / Protein Ycf2 / Aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit B / At4g28210 / ATP-dependent zinc metalloprotease FTSH 12, chloroplastic / Malate dehydrogenase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiang, K. / Zhan, X. / Xu, Q. / Wu, J. / Yan, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271239 China
CitationJournal: Cell / Year: 2024
Title: Structural insights into the chloroplast protein import in land plants.
Authors: Ke Liang / Zeyu Jin / Xiechao Zhan / Yuxin Li / Qikui Xu / Yanqiu Xie / Yi Yang / Shaojie Wang / Jianping Wu / Zhen Yan /
Abstract: Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi ...Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi complex has been identified as the chloroplast import motor. However, its assembly and cooperation with the TIC complex during preprotein translocation remain unclear. Here, we present the structures of the Ycf2-FtsHi and TIC complexes from Arabidopsis and an ultracomplex formed between them from Pisum. The Ycf2-FtsHi structure reveals a heterohexameric AAA+ ATPase motor module with characteristic features. Four previously uncharacterized components of Ycf2-FtsHi were identified, which aid in complex assembly and anchoring of the motor module at a tilted angle relative to the membrane. When considering the structures of the TIC complex and the TIC-Ycf2-FtsHi ultracomplex together, it becomes evident that the tilted motor module of Ycf2-FtsHi enables its close contact with the TIC complex, thereby facilitating efficient preprotein translocation. Our study provides valuable structural insights into the chloroplast protein import process in land plants.
History
DepositionDec 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable inactive ATP-dependent zinc metalloprotease FTSHI 4, chloroplastic
B: ATP-dependent zinc metalloprotease FTSH 12, chloroplastic
C: Probable inactive ATP-dependent zinc metalloprotease FTSHI 5, chloroplastic
D: Protein Ycf2
E: Probable inactive ATP-dependent zinc metalloprotease FTSHI 1, chloroplastic
F: Probable inactive ATP-dependent zinc metalloprotease FTSHI 2, chloroplastic
G: AtTam46
H: At4g28210
I: Malate dehydrogenase, chloroplastic
J: Malate dehydrogenase, chloroplastic
K: Aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit B
L: UNK
M: UNK
N: UNK
O: UNK
P: UNK
R: Embryo defective 2737
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,067,46321
Polymers1,066,73117
Non-polymers7324
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Probable inactive ATP-dependent zinc metalloprotease FTSHI ... , 4 types, 4 molecules ACEF

#1: Protein Probable inactive ATP-dependent zinc metalloprotease FTSHI 4, chloroplastic / AtFTSHI4 / Protein EMBRYO DEFECTIVE 3144 / Protein FTSH INACTIVE PROTEASE 4


Mass: 96975.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4KF14
#3: Protein Probable inactive ATP-dependent zinc metalloprotease FTSHI 5, chloroplastic / AtFTSHI5 / Protein EMBRYO DEFECTIVE 2458 / Protein FTSH INACTIVE PROTEASE 5


Mass: 152479.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4J3N2
#5: Protein Probable inactive ATP-dependent zinc metalloprotease FTSHI 1, chloroplastic / AtFTSHI1 / Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 1 / Protein ARC1 / Protein FTSH ...AtFTSHI1 / Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 1 / Protein ARC1 / Protein FTSH INACTIVE PROTEASE 1


Mass: 105677.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O22993
#6: Protein Probable inactive ATP-dependent zinc metalloprotease FTSHI 2, chloroplastic / AtFTSHI2 / Protein EMBRYO DEFECTIVE 2083 / Protein FTSH INACTIVE PROTEASE 2


Mass: 100019.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A8MPR5

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Protein , 7 types, 8 molecules BDGHIJKR

#2: Protein ATP-dependent zinc metalloprotease FTSH 12, chloroplastic / AtFTSH12


Mass: 115267.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9SAJ3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#4: Protein Protein Ycf2


Mass: 269925.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56786
#7: Protein AtTam46


Mass: 45844.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#8: Protein At4g28210 / Embryo defective 1923


Mass: 38379.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M0I6
#9: Protein Malate dehydrogenase, chloroplastic / Chloroplastic malate dehydrogenase / Chloroplastic MDH / cpNAD-MDH / Plastidic NAD-dependent malate ...Chloroplastic malate dehydrogenase / Chloroplastic MDH / cpNAD-MDH / Plastidic NAD-dependent malate dehydrogenase / pNAD-MDH


Mass: 42452.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SN86, malate dehydrogenase
#10: Protein Aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit B / At5g22210


Mass: 9327.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C567
#16: Protein Embryo defective 2737


Mass: 37382.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4JYR0

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Protein/peptide , 5 types, 5 molecules LMNOP

#11: Protein/peptide UNK


Mass: 1962.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#12: Protein/peptide UNK


Mass: 1232.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#13: Protein/peptide UNK


Mass: 3781.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#14: Protein/peptide UNK


Mass: 1934.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#15: Protein/peptide UNK


Mass: 1635.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)

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Non-polymers , 2 types, 4 molecules

#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#18: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H52O8P

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Details

Has ligand of interestN
Has protein modificationN

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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 Ycf2-FtsHi motor complex from Arabidopsis / Type: COMPLEX
Entity ID: #2, #9, #4, #1, #5, #3, #7, #6, #16, #8, #10, #13, #12, #11, #14-#15
Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 340640 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00446341
ELECTRON MICROSCOPYf_angle_d0.79262626
ELECTRON MICROSCOPYf_dihedral_angle_d5.1566180
ELECTRON MICROSCOPYf_chiral_restr0.0457031
ELECTRON MICROSCOPYf_plane_restr0.0067983

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