[English] 日本語
Yorodumi
- EMDB-36938: Outward-facing structure of human ABCB6 W546A mutant (ADP/VO4-bound) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36938
TitleOutward-facing structure of human ABCB6 W546A mutant (ADP/VO4-bound)
Map data
Sample
  • Organelle or cellular component: ATP-binding cassette sub-family B member 6 - Homo sapiens
    • Protein or peptide: ATP-binding cassette sub-family B member 6
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: MAGNESIUM ION
KeywordsATP-Binding Cassette transporter / mitochondrial transporter / outward-facing state / ADP/VO4-bound / ABCB6 / MEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


cellular detoxification of cadmium ion / Defective ABCB6 causes MCOPCB7 / heme transmembrane transport / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / ABC-type heme transporter activity / porphyrin-containing compound metabolic process / tetrapyrrole binding / heme transport ...cellular detoxification of cadmium ion / Defective ABCB6 causes MCOPCB7 / heme transmembrane transport / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / ABC-type heme transporter activity / porphyrin-containing compound metabolic process / tetrapyrrole binding / heme transport / heme metabolic process / porphyrin-containing compound biosynthetic process / melanosome assembly / melanosome membrane / multivesicular body membrane / mitochondrial envelope / endolysosome membrane / vacuolar membrane / skin development / efflux transmembrane transporter activity / intracellular copper ion homeostasis / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex / brain development / transmembrane transport / early endosome membrane / intracellular iron ion homeostasis / mitochondrial outer membrane / endosome / lysosomal membrane / Golgi membrane / heme binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Mitochondrial ABC-transporter, N-terminal five TM domain / Mitochondrial ABC-transporter N-terminal five TM region / 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 ...Mitochondrial ABC-transporter, N-terminal five TM domain / Mitochondrial ABC-transporter N-terminal five TM region / 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
ATP-binding cassette sub-family B member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJin MS / Lee SS / Park JG / Jang E / Choi SH / Kim S / Kim JW
Funding support Korea, Republic Of, 3 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019M3E5D6063908 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4022846 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1A2C1091278 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2023
Title: W546 stacking disruption traps the human porphyrin transporter ABCB6 in an outward-facing transient state.
Authors: Sang Soo Lee / Jun Gyou Park / Eunhong Jang / Seung Hun Choi / Subin Kim / Ji Won Kim / Mi Sun Jin /
Abstract: Human ATP-binding cassette transporter subfamily B6 (ABCB6) is a mitochondrial ATP-driven pump that translocates porphyrins from the cytoplasm into mitochondria for heme biosynthesis. Within the ...Human ATP-binding cassette transporter subfamily B6 (ABCB6) is a mitochondrial ATP-driven pump that translocates porphyrins from the cytoplasm into mitochondria for heme biosynthesis. Within the transport pathway, a conserved aromatic residue W546 located in each monomer plays a pivotal role in stabilizing the occluded conformation via π-stacking interactions. Herein, we employed cryo-electron microscopy to investigate the structural consequences of a single W546A mutation in ABCB6, both in detergent micelles and nanodiscs. The results demonstrate that the W546A mutation alters the conformational dynamics of detergent-purified ABCB6, leading to entrapment of the transporter in an outward-facing transient state. However, in the nanodisc system, we observed a direct interaction between the transporter and a phospholipid molecule that compensates for the absence of the W546 residue, thereby facilitating the normal conformational transition of the transporter toward the occluded state following ATP hydrolysis. The findings also reveal that adoption of the outward-facing conformation causes charge repulsion between ABCB6 and the bound substrate, and rearrangement of key interacting residues at the substrate-binding site. Consequently, the affinity for the substrate is significantly reduced, facilitating its release from the transporter.
History
DepositionJul 26, 2023-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36938.png

Downloads & links

-
Map

FileDownload / File: emd_36938.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.851 Å
Density
Contour LevelBy AUTHOR: 0.136
Minimum - Maximum-0.7837791 - 1.0213846
Average (Standard dev.)0.003889776 (±0.041191142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 195.73 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_36938_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_36938_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ATP-binding cassette sub-family B member 6 - Homo sapiens

EntireName: ATP-binding cassette sub-family B member 6 - Homo sapiens
Components
  • Organelle or cellular component: ATP-binding cassette sub-family B member 6 - Homo sapiens
    • Protein or peptide: ATP-binding cassette sub-family B member 6
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: ATP-binding cassette sub-family B member 6 - Homo sapiens

SupramoleculeName: ATP-binding cassette sub-family B member 6 - Homo sapiens
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: ATP-binding cassette sub-family B member 6

MacromoleculeName: ATP-binding cassette sub-family B member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type heme transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.869797 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: RDFGRKLRLL SGYLWPRGSP ALQLVVLICL GLMGLERALN VLVPIFYRNI VNLLTEKAPW NSLAWTVTSY VFLKFLQGGG TGSTGFVSN LRTFLWIRVQ QFTSRRVELL IFSHLHELSL RWHLGRRTGE VLRIADRGTS SVTGLLSYLV FNVIPTLADI I IGIIYFSM ...String:
RDFGRKLRLL SGYLWPRGSP ALQLVVLICL GLMGLERALN VLVPIFYRNI VNLLTEKAPW NSLAWTVTSY VFLKFLQGGG TGSTGFVSN LRTFLWIRVQ QFTSRRVELL IFSHLHELSL RWHLGRRTGE VLRIADRGTS SVTGLLSYLV FNVIPTLADI I IGIIYFSM FFNAWFGLIV FLCMSLYLTL TIVVTEWRTK FRRAMNTQEN ATRARAVDSL LNFETVKYYN AESYEVERYR EA IIKYQGL EWKSSASLVL LNQTQNLVIG LGLLAGSLLC AYFVTEQKLQ VGDYVLFGTY IIQLYMPLNA FGTYYRMIQT NFI DMENMF DLLKEETEVK DLPGAGPLRF QKGRIEFENV HFSYADGRET LQDVSFTVMP GQTLALVGPS GAGKSTILRL LFRF YDISS GCIRIDGQDI SQVTQASLRS HIGVVPQDTV LFNDTIADNI RYGRVTAGND EVEAAAQAAG IHDAIMAFPE GYRTQ VGER GLKLSGGEKQ RVAIARTILK APGIILLDEA TSALDTSNER AIQASLAKVC ANRTTIVVAH RLSTVVNADQ ILVIKD GCI VERGRHEALL SRGGVYADMW QLQQ

UniProtKB: ATP-binding cassette sub-family B member 6

-
Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

-
Macromolecule #3: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION / Vanadate

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56293
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more