This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6rfq

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 05:39, 11 April 2020

Cryo-EM structure of a respiratory complex I assembly intermediate with NDUFAF2

6rfq, resolution 3.30Å

Structural highlights

6rfq is a 41 chain structure with sequence from Yarrowia lipolytica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Activity:	NADH dehydrogenase, with EC number 1.6.99.3
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[Q9UUU2_YARLL] Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain.[RuleBase:RU364066] [A0A371C2D0_YARLL] Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.[PIRNR:PIRNR017016] [A0A1H6PXT9_YARLL] Carrier of the growing fatty acid chain in fatty acid biosynthesis.[RuleBase:RU000722] [NU6M_YARLI] Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. [S5TMS4_YARLL] Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.[RuleBase:RU003640][SAAS:SAAS01013641] [NU4LM_YARLI] Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. [A0A1D8NG21_YARLL] Carrier of the growing fatty acid chain in fatty acid biosynthesis.[RuleBase:RU000722] [S5TF58_YARLL] Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.[RuleBase:RU003404] [S5TMP9_YARLL] Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.[RuleBase:RU003297]

Publication Abstract from PubMed

Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is associated with severe human diseases. Assembly of the one-megadalton complex I in the inner mitochondrial membrane requires assembly factors and chaperones. We have determined the structure of complex I from the aerobic yeast Yarrowia lipolytica by electron cryo-microscopy at 3.2-A resolution. A ubiquinone molecule was identified in the access path to the active site. The electron cryo-microscopy structure indicated an unusual lipid-protein arrangement at the junction of membrane and matrix arms that was confirmed by molecular simulations. The structure of a complex I mutant and an assembly intermediate provide detailed molecular insights into the cause of a hereditary complex I-linked disease and complex I assembly in the inner mitochondrial membrane.

High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease.,Parey K, Haapanen O, Sharma V, Kofeler H, Zullig T, Prinz S, Siegmund K, Wittig I, Mills DJ, Vonck J, Kuhlbrandt W, Zickermann V Sci Adv. 2019 Dec 11;5(12):eaax9484. doi: 10.1126/sciadv.aax9484. eCollection, 2019 Dec. PMID:31844670^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Parey K, Haapanen O, Sharma V, Kofeler H, Zullig T, Prinz S, Siegmund K, Wittig I, Mills DJ, Vonck J, Kuhlbrandt W, Zickermann V. High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease. Sci Adv. 2019 Dec 11;5(12):eaax9484. doi: 10.1126/sciadv.aax9484. eCollection, 2019 Dec. PMID:31844670 doi:http://dx.doi.org/10.1126/sciadv.aax9484

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6rfq"

@@ Line 3: / Line 3: @@
 <SX load='6rfq' size='340' side='right' viewer='molstar' caption='[[6rfq]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6rfq]] is a 41 chain structure with sequence from [http://en.wikipedia.org/wiki/Yarrowia_lipolytica Yarrowia lipolytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RFQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RFQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6rfq]] is a 41 chain structure with sequence from [http://en.wikipedia.org/wiki/Yarrowia_lipolytica Yarrowia lipolytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RFQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RFQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=CPL:1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>CPL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=LMN:LAURYL+MALTOSE+NEOPENTYL+GLYCOL'>LMN</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PLC:DIUNDECYL+PHOSPHATIDYL+CHOLINE'>PLC</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=T7X:PHOSPHATIDYLINOSITOL'>T7X</scene>, <scene name='pdbligand=ZMP:S-[2-({N-[(2S)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANYL}AMINO)ETHYL]+TETRADECANETHIOATE'>ZMP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=CPL:1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>CPL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=LMN:LAURYL+MALTOSE+NEOPENTYL+GLYCOL'>LMN</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PLC:DIUNDECYL+PHOSPHATIDYL+CHOLINE'>PLC</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=T7X:PHOSPHATIDYLINOSITOL'>T7X</scene>, <scene name='pdbligand=ZMP:S-[2-({N-[(2S)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANYL}AMINO)ETHYL]+TETRADECANETHIOATE'>ZMP</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NADH_dehydrogenase NADH dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.99.3 1.6.99.3] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6rfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rfq OCA], [http://pdbe.org/6rfq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rfq RCSB], [http://www.ebi.ac.uk/pdbsum/6rfq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rfq ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6rfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rfq OCA], [http://pdbe.org/6rfq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rfq RCSB], [http://www.ebi.ac.uk/pdbsum/6rfq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rfq ProSAT]</span></td></tr>
 </table>
 == Function ==

6rfq

From Proteopedia

Revision as of 05:39, 11 April 2020

Cryo-EM structure of a respiratory complex I assembly intermediate with NDUFAF2

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox