+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34091 | |||||||||
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Title | TLR7 in complex with an inhibitor | |||||||||
Map data | ||||||||||
Sample |
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Keywords | TLR7 / antagonist / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information toll-like receptor 7 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of chemokine production ...toll-like receptor 7 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of chemokine production / JNK cascade / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / regulation of protein phosphorylation / cellular response to virus / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of interleukin-6 production / positive regulation of type II interferon production / double-stranded RNA binding / defense response to virus / single-stranded RNA binding / lysosome / receptor complex / endosome / inflammatory response / innate immune response / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Macaca mulatta (Rhesus monkey) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.77 Å | |||||||||
Authors | Zhang Z / Ohto U / Shimizu T | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: TLR7 in complex with an inhibitor Authors: Zhang Z / Shimizu T | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34091.map.gz | 14.6 MB | EMDB map data format | |
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Header (meta data) | emd-34091-v30.xml emd-34091.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34091_fsc.xml | 5.7 KB | Display | FSC data file |
Images | emd_34091.png | 160.4 KB | ||
Filedesc metadata | emd-34091.cif.gz | 5.8 KB | ||
Others | emd_34091_additional_1.map.gz emd_34091_half_map_1.map.gz emd_34091_half_map_2.map.gz | 11.2 MB 11.2 MB 11.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34091 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34091 | HTTPS FTP |
-Validation report
Summary document | emd_34091_validation.pdf.gz | 914 KB | Display | EMDB validaton report |
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Full document | emd_34091_full_validation.pdf.gz | 913.5 KB | Display | |
Data in XML | emd_34091_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_34091_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34091 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34091 | HTTPS FTP |
-Related structure data
Related structure data | 7ytpMC 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_34091.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_34091_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34091_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34091_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TLR7 in complex with an inhibitor
Entire | Name: TLR7 in complex with an inhibitor |
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Components |
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-Supramolecule #1: TLR7 in complex with an inhibitor
Supramolecule | Name: TLR7 in complex with an inhibitor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: Toll-like receptor 7
Macromolecule | Name: Toll-like receptor 7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 111.561273 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: MKLCILLAVV AFVGLSLGRS PWARWFPKTL PCDVTLDVSK NHVIVDCTDK HLTEIPGGIP TNTTNLTLTI NHIPDISPAS FHRLVHLVE IDFRCNCVPI RLGSKSNMCP RRLQIKPRSF SGLTYLKSLY LDGNQLLEIP QGLPPSLQLL SLEANNIFSI R KEQLTELA ...String: MKLCILLAVV AFVGLSLGRS PWARWFPKTL PCDVTLDVSK NHVIVDCTDK HLTEIPGGIP TNTTNLTLTI NHIPDISPAS FHRLVHLVE IDFRCNCVPI RLGSKSNMCP RRLQIKPRSF SGLTYLKSLY LDGNQLLEIP QGLPPSLQLL SLEANNIFSI R KEQLTELA NIEILYLGQN CYYRNPCYVS YSIEKDAFLN LTKLKVLSLK DNNVTTVPTV LPSTLTELYL YNNMIAEIQE DD FNNLNQL QILDLSGNCP RCYNAPFPCT PCKNNSPLQI PVNAFDALTE LKVLRLHSNS LQHVPPRWFK NINNLQELDL SQN FLAKEI GDAKFLHFLP NLIQLDLSFN FELQVYRASM NLSQAFSSLK SLKILRIRGY VFKELKSFQL SPLHNLQNLE VLDL GTNFI KIANLSMFKQ FKRLKVIDLS VNKISPSGDS LVPRGSSNAR TSVESYEPQV LEQLYYFRYD KYARSCRFKN KEASF TSVQ ESCYKYGQTL DLSKNSIFFI KSSDFQHLSF LKCLNLSGNL ISQTLNGSEF QPLAELRYLD FSNNRLDLLH STAFEE LRK LEVLDISSNS HYFQSEGITH MLNFTKNLKV LQKLMMNDND ISSSTSRTME SESLRTLEFR GNHLDVLWRD GDNRYLQ LF KNLLKLEELD ISKNSLSFLP SGVFDGMPPN LKNLSLAKNG LKSFIWEKLR YLKNLETLDL SHNQLTTVPE RLSNCSRS L KNLILKNNQI RSLTKYFLQD AFQLRYLDLS SNKIQMIQKT SFPENVLNNL KMLLLHHNRF LCTCDAVWFV WWVQHTEVT IPYLATDVTC VGPGAHKGQS VISLDLYTCE LDLTNEFLVP RGSAAQHDEA VDNKFNKEQQ NAFYEILHLP NLNEEQRNAF IQSLKDDPS QSANLLAEAK KLNDAQAPKV DNKFNKEQQN AFYEILHLPN LNEEQRNAFI QSLKDDPSQS ANLLAEAKKL N DAQAPKVD ANSSSVP UniProtKB: Toll-like receptor 7 |
-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: 10 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: (2R,6R)-4-(8-cyanoquinolin-5-yl)-N-[(3S,4R)-4-fluoranylpyrrolidin...
Macromolecule | Name: (2R,6R)-4-(8-cyanoquinolin-5-yl)-N-[(3S,4R)-4-fluoranylpyrrolidin-3-yl]-6-methyl-morpholine-2-carboxamide type: ligand / ID: 4 / Number of copies: 2 / Formula: JRI |
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Molecular weight | Theoretical: 383.419 Da |
Chemical component information | ChemComp-JRI: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 4.8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 61.1 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: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |