+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28864 | |||||||||
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Title | Human ABCA4 structure in complex with AMP-PNP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ABC transporter / importer / membrane protein / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information rod photoreceptor disc membrane / flippase activity / N-retinylidene-phosphatidylethanolamine flippase activity / all-trans retinal binding / phospholipid transfer to membrane / retinol transmembrane transporter activity / phospholipid transporter activity / 11-cis retinal binding / retinal metabolic process / ATPase-coupled intramembrane lipid transporter activity ...rod photoreceptor disc membrane / flippase activity / N-retinylidene-phosphatidylethanolamine flippase activity / all-trans retinal binding / phospholipid transfer to membrane / retinol transmembrane transporter activity / phospholipid transporter activity / 11-cis retinal binding / retinal metabolic process / ATPase-coupled intramembrane lipid transporter activity / phosphatidylethanolamine flippase activity / phototransduction, visible light / retinoid binding / photoreceptor cell maintenance / P-type phospholipid transporter / lipid transport / phospholipid translocation / retinoid metabolic process / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / photoreceptor outer segment / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / visual perception / ABC-family proteins mediated transport / transmembrane transport / photoreceptor disc membrane / cytoplasmic vesicle / intracellular membrane-bounded organelle / GTPase activity / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.95 Å | |||||||||
Authors | Scortecci JF / Van Petegem F / Molday RS | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: To Be Published Title: Structural and Functional Characterization of ABCA4 in its Nucleotide-Bound State Authors: Scortecci JF / Garces FA / Molday LL / Van Petegem F / Molday RS | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28864.map.gz | 89.2 MB | EMDB map data format | |
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Header (meta data) | emd-28864-v30.xml emd-28864.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_28864.png | 13.8 KB | ||
Filedesc metadata | emd-28864.cif.gz | 7.1 KB | ||
Others | emd_28864_half_map_1.map.gz emd_28864_half_map_2.map.gz | 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28864 | HTTPS FTP |
-Validation report
Summary document | emd_28864_validation.pdf.gz | 875.3 KB | Display | EMDB validaton report |
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Full document | emd_28864_full_validation.pdf.gz | 874.8 KB | Display | |
Data in XML | emd_28864_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | emd_28864_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28864 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28864 | HTTPS FTP |
-Related structure data
Related structure data | 8f5bMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28864.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04903 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28864_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28864_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ABCA4 structure in complex with AMP-PNP
Entire | Name: ABCA4 structure in complex with AMP-PNP |
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Components |
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-Supramolecule #1: ABCA4 structure in complex with AMP-PNP
Supramolecule | Name: ABCA4 structure in complex with AMP-PNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Recombinantly expressed human ABCA4 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Retinal-specific phospholipid-transporting ATPase ABCA4
Macromolecule | Name: Retinal-specific phospholipid-transporting ATPase ABCA4 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type phospholipid transporter |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 256.202531 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGFVRQIQLL LWKNWTLRKR QKIRFVVELV WPLSLFLVLI WLRNANPLYS HHECHFPNKA MPSAGMLPWL QGIFCNVNNP CFQSPTPGE SPGIVSNYNN SILARVYRDF QELLMNAPES QHLGRIWTEL HILSQFMDTL RTHPERIAGR GIRIRDILKD E ETLTLFLI ...String: MGFVRQIQLL LWKNWTLRKR QKIRFVVELV WPLSLFLVLI WLRNANPLYS HHECHFPNKA MPSAGMLPWL QGIFCNVNNP CFQSPTPGE SPGIVSNYNN SILARVYRDF QELLMNAPES QHLGRIWTEL HILSQFMDTL RTHPERIAGR GIRIRDILKD E ETLTLFLI KNIGLSDSVV YLLINSQVRP EQFAHGVPDL ALKDIACSEA LLERFIIFSQ RRGAKTVRYA LCSLSQGTLQ WI EDTLYAN VDFFKLFRVL PTLLDSRSQG INLRSWGGIL SDMSPRIQEF IHRPSMQDLL WVTRPLMQNG GPETFTKLMG ILS DLLCGY PEGGGSRVLS FNWYEDNNYK AFLGIDSTRK DPIYSYDRRT TSFCNALIQS LESNPLTKIA WRAAKPLLMG KILY TPDSP AARRILKNAN STFEELEHVR KLVKAWEEVG PQIWYFFDNS TQMNMIRDTL GNPTVKDFLN RQLGEEGITA EAILN FLYK GPRESQADDM ANFDWRDIFN ITDRTLRLVN QYLECLVLDK FESYNDETQL TQRALSLLEE NMFWAGVVFP DMYPWT SSL PPHVKYKIRM DIDVVEKTNK IKDRYWDSGP RADPVEDFRY IWGGFAYLQD MVEQGITRSQ VQAEAPVGIY LQQMPYP CF VDDSFMIILN RCFPIFMVLA WIYSVSMTVK SIVLEKELRL KETLKNQGVS NAVIWCTWFL DSFSIMSMSI FLLTIFIM H GRILHYSDPF ILFLFLLAFS TATIMLCFLL STFFSKASLA AACSGVIYFT LYLPHILCFA WQDRMTAELK KAVSLLSPV AFGFGTEYLV RFEEQGLGLQ WSNIGNSPTE GDEFSFLLSM QMMLLDAAVY GLLAWYLDQV FPGDYGTPLP WYFLLQESYW LGGEGCSTR EERALEKTEP LTEETEDPEH PEGIHDSFFE REHPGWVPGV CVKNLVKIFE PCGRPAVDRL NITFYENQIT A FLGHNGAG KTTTLSILTG LLPPTSGTVL VGGRDIETSL DAVRQSLGMC PQHNILFHHL TVAEHMLFYA QLKGKSQEEA QL EMEAMLE DTGLHHKRNE EAQDLSGGMQ RKLSVAIAFV GDAKVVILDE PTSGVDPYSR RSIWDLLLKY RSGRTIIMST HHM DEADLL GDRIAIIAQG RLYCSGTPLF LKNCFGTGLY LTLVRKMKNI QSQRKGSEGT CSCSSKGFST TCPAHVDDLT PEQV LDGDV NELMDVVLHH VPEAKLVECI GQELIFLLPN KNFKHRAYAS LFRELEETLA DLGLSSFGIS DTPLEEIFLK VTEDS DSGP LFAGGAQQKR ENVNPRHPCL GPREKAGQTP QDSNVCSPGA PAAHPEGQPP PEPECPGPQL NTGTQLVLQH VQALLV KRF QHTIRSHKDF LAQIVLPATF VFLALMLSIV IPPFGEYPAL TLHPWIYGQQ YTFFSMDEPG SEQFTVLADV LLNKPGF GN RCLKEGWLPE YPCGNSTPWK TPSVSPNITQ LFQKQKWTQV NPSPSCRCST REKLTMLPEC PEGAGGLPPP QRTQRSTE I LQDLTDRNIS DFLVKTYPAL IRSSLKSKFW VNEQRYGGIS IGGKLPVVPI TGEALVGFLS DLGRIMNVSG GPITREASK EIPDFLKHLE TEDNIKVWFN NKGWHALVSF LNVAHNAILR ASLPKDRSPE EYGITVISQP LNLTKEQLSE ITVLTTSVDA VVAICVIFS MSFVPASFVL YLIQERVNKS KHLQFISGVS PTTYWVTNFL WDIMNYSVSA GLVVGIFIGF QKKAYTSPEN L PALVALLL LYGWAVIPMM YPASFLFDVP STAYVALSCA NLFIGINSSA ITFILELFEN NRTLLRFNAV LRKLLIVFPH FC LGRGLID LALSQAVTDV YARFGEEHSA NPFHWDLIGK NLFAMVVEGV VYFLLTLLVQ RHFFLSQWIA EPTKEPIVDE DDD VAEERQ RIITGGNKTD ILRLHELTKI YPGTSSPAVD RLCVGVRPGE CFGLLGVNGA GKTTTFKMLT GDTTVTSGDA TVAG KSILT NISEVHQNMG YCPQFDAIDE LLTGREHLYL YARLRGVPAE EIEKVANWSI KSLGLTVYAD CLAGTYSGGN KRKLS TAIA LIGCPPLVLL DEPTTGMDPQ ARRMLWNVIV SIIREGRAVV LTSHSMEECE ALCTRLAIMV KGAFRCMGTI QHLKSK FGD GYIVTMKIKS PKDDLLPDLN PVEQFFQGNF PGSVQRERHY NMLQFQVSSS SLARIFQLLL SHKDSLLIEE YSVTQTT LD QVFVNFAKQQ TESHDLPLHP RAAGASRQAQ D UniProtKB: Retinal-specific phospholipid-transporting ATPase ABCA4 |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |