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Yorodumi- EMDB-30527: Acinetobacter MlaFEDB complex in ATP-bound Vtrans2 conformation -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30527 | |||||||||
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Title | Acinetobacter MlaFEDB complex in ATP-bound Vtrans2 conformation | |||||||||
Map data | cryo EM map of the Acinetobacter MlaFEDB complex in ATP-bound Vtrans2 conformation | |||||||||
Sample |
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Keywords | MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Zhang YY / Fan QX | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Discov / Year: 2020 Title: Cryo-EM structures of Acinetobacter baumannii glycerophospholipid transporter. Authors: Yuanyuan Zhang / Qiongxuan Fan / Ximin Chi / Qiang Zhou / Yanyan Li / | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30527.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-30527-v30.xml emd-30527.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_30527.png | 52.6 KB | ||
Filedesc metadata | emd-30527.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30527 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30527 | HTTPS FTP |
-Related structure data
Related structure data | 7d09MC 7d06C 7d08C 7d0aC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30527.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryo EM map of the Acinetobacter MlaFEDB complex in ATP-bound Vtrans2 conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Acinetobacter MlaFEDB complex in ATP-bound Vtrans2 conformation
Entire | Name: Acinetobacter MlaFEDB complex in ATP-bound Vtrans2 conformation |
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Components |
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-Supramolecule #1: Acinetobacter MlaFEDB complex in ATP-bound Vtrans2 conformation
Supramolecule | Name: Acinetobacter MlaFEDB complex in ATP-bound Vtrans2 conformation type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
-Macromolecule #1: Intermembrane phospholipid transport system permease protein MlaE
Macromolecule | Name: Intermembrane phospholipid transport system permease protein MlaE type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Molecular weight | Theoretical: 27.322443 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MNTIAWLGRL VIERIRGIGV AALMLLQIIF SLPSAGGFGR FVYQMHRVGV MSLLIITVSG LFIGLVLGLQ GYSILVNVGS ESMLGTMVS LTLLRELAPV VAALLFAGRA GSALTAEIGS MKQSEQLASM EMIGVDPLKQ IVSPRLWAGI VSLPMLTVIF A AIGIVGGK ...String: MNTIAWLGRL VIERIRGIGV AALMLLQIIF SLPSAGGFGR FVYQMHRVGV MSLLIITVSG LFIGLVLGLQ GYSILVNVGS ESMLGTMVS LTLLRELAPV VAALLFAGRA GSALTAEIGS MKQSEQLASM EMIGVDPLKQ IVSPRLWAGI VSLPMLTVIF A AIGIVGGK LVGVDFLGVD EGSFWSGMQN NVQFGHDVVN GIIKSIVFAL LCTWIAVFQG YACDPTPEGI ATAMTRTVVY SS LCVLGFD FVLTAVMFGG I UniProtKB: Intermembrane phospholipid transport system permease protein MlaE |
-Macromolecule #2: ABC transporter ATP-binding protein
Macromolecule | Name: ABC transporter ATP-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Molecular weight | Theoretical: 30.070455 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MMNNKTPLST QSLIEVKNLS FNRGERVIYD NISLNIRRGQ ITAIMGPSGT GKTTLLRLIG GQLVPDQGEV LLDGKDIAQM SRQELFAAR ARMGMLFQSG ALFTDMSVYE NVAFPIRAHT KLSENLIAEL VALKLESVGL RGTEQLMPTE LSGGMNRRVA L ARAIALDP ...String: MMNNKTPLST QSLIEVKNLS FNRGERVIYD NISLNIRRGQ ITAIMGPSGT GKTTLLRLIG GQLVPDQGEV LLDGKDIAQM SRQELFAAR ARMGMLFQSG ALFTDMSVYE NVAFPIRAHT KLSENLIAEL VALKLESVGL RGTEQLMPTE LSGGMNRRVA L ARAIALDP DLIMYDEPFA GQDPIVKGVL TRLIRSLREA LDLTTIIVSH DVPETLSIAD YIYVVAEGKI QGEGTPEELQ AY ASPFVKQ FLTGSAEGPV EYQFSHQAYL DNEVRP UniProtKB: ABC transporter ATP-binding protein |
-Macromolecule #3: Anti-sigma factor antagonist
Macromolecule | Name: Anti-sigma factor antagonist / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Molecular weight | Theoretical: 11.91376 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: VVQYLNQELV VSGKIDFENA EQQYQAGLAI IKKQTSFPLI VDLKQLEHGN TLALAVLVQW LRQTPQKSGL HFKNVPEKML KIIQACHLQ EDLHLVLEHH HHHH UniProtKB: Anti-sigma factor antagonist |
-Macromolecule #4: MCE family protein
Macromolecule | Name: MCE family protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Molecular weight | Theoretical: 24.135322 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MKSRTSELAV GIFVIIFGIA LFFLAMKVSG LVGTNLSDGY TMKAQFDNVN GLKPRAKVTM SGVTIGRVDS ITLDPVTRLA TVTFDLDGK LTSFNAEQLK EVQKNALDEL RYSSDYTQAT PAQQKTMEQQ LISNMNSITS IDEDAYIMVA TNGLLGEKYL K IVPGGGLN ...String: MKSRTSELAV GIFVIIFGIA LFFLAMKVSG LVGTNLSDGY TMKAQFDNVN GLKPRAKVTM SGVTIGRVDS ITLDPVTRLA TVTFDLDGK LTSFNAEQLK EVQKNALDEL RYSSDYTQAT PAQQKTMEQQ LISNMNSITS IDEDAYIMVA TNGLLGEKYL K IVPGGGLN YLKRGDTISN TQGTMDLEDL ISKFITGGGA GKVAAGSSSA EEKAPASTDS SAQPSFVE UniProtKB: ABC transporter periplasmic substrate-binding protein |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film 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 model | Type of model: OTHER |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 52789 |