[English] 日本語
Yorodumi- EMDB-41621: Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41621 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosphate (IP4) | ||||||||||||||||||
Map data | Sharpened map of P-Rex1 bound to IP4 | ||||||||||||||||||
Sample |
| ||||||||||||||||||
Keywords | Rho guanine-nucleotide exchange factor / Dbl homology domain / pleckstrin homology domain / Phosphatidylinositol 3 / 4 / 5-trisphosphate binding / SIGNALING PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information regulation of signaling / regulation of dendrite development / neutrophil activation / regulation of actin filament polymerization / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / superoxide metabolic process / NRAGE signals death through JNK / RHOC GTPase cycle / RHOJ GTPase cycle ...regulation of signaling / regulation of dendrite development / neutrophil activation / regulation of actin filament polymerization / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / superoxide metabolic process / NRAGE signals death through JNK / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / T cell differentiation / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / RAC1 GTPase cycle / neutrophil chemotaxis / actin filament polymerization / GTPase activator activity / guanyl-nucleotide exchange factor activity / dendritic shaft / phospholipid binding / G alpha (12/13) signalling events / growth cone / positive regulation of cell migration / intracellular signal transduction / G protein-coupled receptor signaling pathway / perinuclear region of cytoplasm / enzyme binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||||||||
Authors | Cash JN / Tesmer JJG | ||||||||||||||||||
Funding support | United States, 5 items
| ||||||||||||||||||
Citation | Journal: Nat Methods / Year: 2020 Title: Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Authors: Ali Punjani / Haowei Zhang / David J Fleet / Abstract: Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are ...Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are often kept in solution with detergent micelles and lipid nanodiscs that are locally disordered. Such spatial variability negatively impacts computational three-dimensional (3D) reconstruction with existing iterative refinement algorithms that assume rigidity. We introduce non-uniform refinement, an algorithm based on cross-validation optimization, which automatically regularizes 3D density maps during refinement to account for spatial variability. Unlike common shift-invariant regularizers, non-uniform refinement systematically removes noise from disordered regions, while retaining signal useful for aligning particle images, yielding dramatically improved resolution and 3D map quality in many cases. We obtain high-resolution reconstructions for multiple membrane proteins as small as 100 kDa, demonstrating increased effectiveness of cryo-EM for this class of targets critical in structural biology and drug discovery. Non-uniform refinement is implemented in the cryoSPARC software package. | ||||||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_41621.map.gz | 85.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-41621-v30.xml emd-41621.xml | 25.3 KB 25.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41621_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_41621.png | 162.5 KB | ||
Masks | emd_41621_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-41621.cif.gz | 8.2 KB | ||
Others | emd_41621_half_map_1.map.gz emd_41621_half_map_2.map.gz | 84.5 MB 84.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41621 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41621 | HTTPS FTP |
-Validation report
Summary document | emd_41621_validation.pdf.gz | 868.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_41621_full_validation.pdf.gz | 867.9 KB | Display | |
Data in XML | emd_41621_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_41621_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41621 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41621 | HTTPS FTP |
-Related structure data
Related structure data | 8tuaMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_41621.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map of P-Rex1 bound to IP4 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_41621_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map of P-Rex1 bound to IP4
File | emd_41621_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map of P-Rex1 bound to IP4 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map of P-Rex1 bound to IP4
File | emd_41621_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map of P-Rex1 bound to IP4 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Complex of full-length Phosphatidylinositol 3,4,5-trisphosphate (...
Entire | Name: Complex of full-length Phosphatidylinositol 3,4,5-trisphosphate (PIP3)-dependent Rac exchanger 1 (P-Rex1) bound to inositol 1,3,4,5-tetrakisphosphate (IP4) |
---|---|
Components |
|
-Supramolecule #1: Complex of full-length Phosphatidylinositol 3,4,5-trisphosphate (...
Supramolecule | Name: Complex of full-length Phosphatidylinositol 3,4,5-trisphosphate (PIP3)-dependent Rac exchanger 1 (P-Rex1) bound to inositol 1,3,4,5-tetrakisphosphate (IP4) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 183 KDa |
-Macromolecule #1: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger ...
Macromolecule | Name: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein type: protein_or_peptide / ID: 1 / Details: Inositol 1,3,4,5-tetrakisphosphate / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 183.459484 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GEFAAARESE RQLRLRLCVL NEILGTERDY VGTLRFLQSA FLHRIRQNVA DSVEKGLTEE NVKVLFSNIE DILEVHKDFL AALEYCLHP EPQSQHELGN VFLKFKDKFC VYEEYCSNHE KALRLLVELN KIPTVRAFLL SCMLLGGRKT TDIPLEGYLL S PIQRICKY ...String: GEFAAARESE RQLRLRLCVL NEILGTERDY VGTLRFLQSA FLHRIRQNVA DSVEKGLTEE NVKVLFSNIE DILEVHKDFL AALEYCLHP EPQSQHELGN VFLKFKDKFC VYEEYCSNHE KALRLLVELN KIPTVRAFLL SCMLLGGRKT TDIPLEGYLL S PIQRICKY PLLLKELAKR TPGKHPDHPA VQSALQAMKT VCSNINETKR QMEKLEALEQ LQSHIEGWEG SNLTDICTQL LL QGTLLKI SAGNIQERAF FLFDNLLVYC KRKSRVTGSK KSTKRTKSIN GSLYIFRGRI NTEVMEVENV EDGTADYHSN GYT VTNGWK IHNTAKNKWF VCMAKTAEEK QKWLDAIIRE REQRESLKLG MERDAYVMIA EKGEKLYHMM MNKKVNLIKD RRRK LSTVP KCFLGNEFVA WLLEIGEISK TEEGVNLGQA LLENGIIHHV SDKHQFKNEQ VMYRFRYDDG TYKARSELED IMSKG VRLY CRLHSLYTPV IKDRDYHLKT YKSVLPGSKL VDWLLAQGDC QTREEAVALG VGLCNNGFMH HVLEKSEFRD ESQYFR FHA DEEMEGTSSK NKQLRNDFKL VENILAKRLL ILPQEEDYGF DIEEKNKAVV VKSVQRGSLA EVAGLQVGRK IYSINED LV FLRPFSEVES ILNQSFCSRR PLRLLVATKA KEIIKIPDQP DTLCFQIRGA APPYVYAVGR GSEAMAAGLC AGQCILKV N GSNVMNDGAP EVLEHFQAFR SRREEALGLY QWIYHTHEDA QEARASQEAS TEDPSGEQAQ EEDQADSAFP LLSLGPRLS LCEDSPMVTL TVDNVHLEHG VVYEYVSTAG VRCHVLEKIV EPRGCFGLTA KILEAFAAND SVFVENCRRL MALSSAIVTM PHFEFRNIC DTKLESIGQR IACYQEFAAQ LKSRVSPPFK QAPLEPHPLC GLDFCPTNCH INLMEVSYPK TTPSVGRSFS I RFGRKPSL IGLDPEQGHL NPMSYTQHCI TTMAAPSWKC LPAAEGDPQG QGLHDGSFGP ASGTLGQEDR GLSFLLKQED RE IQDAYLQ LFTKLDVALK EMKQYVTQIN RLLSTITEPT SGGSCDASLA EEASSLPLVS EESEMDRSDH GGIKKVCFKV AEE DQEDSG HDTMSYRDSY SECNSNRDSV LSYTSVRSNS SYLGSDEMGS GDELPCDMRI PSDKQDKLHG CLEHLFNQVD SINA LLKGP VMSRAFEETK HFPMNHSLQE FKQKEECTIR GRSLIQISIQ EDPWNLPNSI KTLVDNIQRY VEDGKNQLLL ALLKC TDTE LQLRRDAIFC QALVAAVCTF SEQLLAALGY RYNNNGEYEE SSRDASRKWL EQVAATGVLL HCQSLLSPAT VKEERT MLE DIWVTLSELD NVTFSFKQLD ENYVANTNVF YHIEGSRQAL KVIFYLDSYH FSKLPSRLEG GASLRLHTAL FTKVLEN VE GLPSPGSQAA EDLQQDINAQ SLEKVQQYYR KLRAFYLERS NLPTDASTTA VKIDQLIRPI NALDELCRLM KSFVHPKP G AAGSVGAGLI PISSELCYRL GACQMVMCGT GMQRSTLSVS LEQAAILARS HGLLPKCIMQ ATDIMRKQGP RVEILAKNL RVKDQMPQGA PRLYRLCQPP VDGDL UniProtKB: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein |
-Macromolecule #2: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
Macromolecule | Name: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: 4IP |
---|---|
Molecular weight | Theoretical: 500.075 Da |
Chemical component information | ChemComp-4IP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.56 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||||||||
Output model | PDB-8tua: |