- EMDB-33603: Cryo-EM Structure of biliverdin-bound mitochondrial ABC transport... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-33603
Title
Cryo-EM Structure of biliverdin-bound mitochondrial ABC transporter ABCB10 from Biortus
Map data
sharpened map
Sample
Complex: Complex of ABCB10 binding with biliverdin
Protein or peptide: ATP-binding cassette sub-family B member 10, mitochondrial
Ligand: CHOLESTEROL
Ligand: Biliverdine IX Alpha
Keywords
ABC transporter / biliverdin / MEMBRANE PROTEIN
Function / homology
Function and homology information
positive regulation of heme biosynthetic process / oligopeptide export from mitochondrion / Mitochondrial ABC transporters / positive regulation of hemoglobin biosynthetic process / ABC-type oligopeptide transporter activity / mitochondrial unfolded protein response / heme biosynthetic process / mitochondrial transport / erythrocyte development / positive regulation of erythrocyte differentiation ...positive regulation of heme biosynthetic process / oligopeptide export from mitochondrion / Mitochondrial ABC transporters / positive regulation of hemoglobin biosynthetic process / ABC-type oligopeptide transporter activity / mitochondrial unfolded protein response / heme biosynthetic process / mitochondrial transport / erythrocyte development / positive regulation of erythrocyte differentiation / mitochondrial membrane / mitochondrial inner membrane / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
Journal: Nat Commun / Year: 2023 Title: Cryo-EM structures of mitochondrial ABC transporter ABCB10 in apo and biliverdin-bound form. Authors: Sheng Cao / Yihu Yang / Lili He / Yumo Hang / Xiaodong Yan / Hui Shi / Jiaquan Wu / Zhuqing Ouyang / Abstract: ABCB10, a member of ABC transporter superfamily that locates in the inner membrane of mitochondria, plays crucial roles in hemoglobin synthesis, antioxidative stress and stabilization of the iron ...ABCB10, a member of ABC transporter superfamily that locates in the inner membrane of mitochondria, plays crucial roles in hemoglobin synthesis, antioxidative stress and stabilization of the iron transporter mitoferrin-1. Recently, it was found that ABCB10 is a mitochondrial biliverdin exporter. However, the molecular mechanism of biliverdin export by ABCB10 remains elusive. Here we report the cryo-EM structures of ABCB10 in apo (ABCB10-apo) and biliverdin-bound form (ABCB10-BV) at 3.67 Å and 2.85 Å resolution, respectively. ABCB10-apo adopts a wide-open conformation and may thus represent the apo form structure. ABCB10-BV forms a closed conformation and biliverdin situates in a hydrophobic pocket in one protomer and bridges the interaction through hydrogen bonds with the opposing one. We also identify cholesterols sandwiched by BVs and discuss the export dynamics based on these structural and biochemical observations.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi