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- EMDB-41621: Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosp... -

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Basic information

Entry
Database: EMDB / ID: EMD-41621
TitleFull-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosphate (IP4)
Map dataSharpened map of P-Rex1 bound to IP4
Sample
  • Complex: 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)
    • Protein or peptide: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
  • Ligand: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
KeywordsRho 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 / NRAGE signals death through JNK / superoxide metabolic process / RHOJ GTPase cycle / RHOC 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 / NRAGE signals death through JNK / superoxide metabolic process / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / T cell differentiation / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / RAC1 GTPase cycle / actin filament polymerization / GTPase activator activity / guanyl-nucleotide exchange factor activity / neutrophil chemotaxis / dendritic shaft / phospholipid binding / G alpha (12/13) signalling events / growth cone / intracellular signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / perinuclear region of cytoplasm / enzyme binding / plasma membrane / cytosol
Similarity search - Function
Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain ...Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsCash JN / Tesmer JJG
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA254402 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA221289 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA023168 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM146664 United States
CitationJournal: 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
DepositionAug 15, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41621.png

Downloads & links

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Map

FileDownload / File: emd_41621.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of P-Rex1 bound to IP4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 288 pix.
= 305.28 Å		1.06 Å/pix.
x 288 pix.
= 305.28 Å		1.06 Å/pix.
x 288 pix.
= 305.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.88094157 - 1.2935833
Average (Standard dev.)0.00012440598 (±0.018127803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 305.27997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41621_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of P-Rex1 bound to IP4

Fileemd_41621_half_map_1.map
AnnotationHalf map of P-Rex1 bound to IP4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of P-Rex1 bound to IP4

Fileemd_41621_half_map_2.map
AnnotationHalf map of P-Rex1 bound to IP4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of full-length Phosphatidylinositol 3,4,5-trisphosphate (...

EntireName: 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
  • Complex: 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)
    • Protein or peptide: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
  • Ligand: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE

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Supramolecule #1: Complex of full-length Phosphatidylinositol 3,4,5-trisphosphate (...

SupramoleculeName: 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 weightTheoretical: 183 KDa

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Macromolecule #1: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger ...

MacromoleculeName: 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 weightTheoretical: 183.459484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE

MacromoleculeName: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: 4IP
Molecular weightTheoretical: 500.075 Da
Chemical component information

ChemComp-4IP:
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.56 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMHEPES
100.0 mMsodium chlorideNaClSodium chloride
2.0 mMDTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2426612
Details: 806,067 particles untilted and 1,620,545 particles tilted
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 187734
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6pcv

chain_id: A, source_name: PDB, initial_model_type: experimental model

6vsk

chain_id: A, source_name: PDB, initial_model_type: experimental model

5d3x

chain_id: A, source_name: PDB, initial_model_type: experimental model

5fi1

chain_id: A, source_name: PDB, initial_model_type: experimental model

7rx9

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8tua:
Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosphate (IP4)

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