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- EMDB-34175: Structure of beta-arrestin2 in complex with a phosphopeptide corr... -

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Basic information

Entry
Database: EMDB / ID: EMD-34175
TitleStructure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human Vasopressin V2 receptor, V2R
Map dataFull map with pixel size 0.82.
Sample
  • Complex: Peptide3 bound beta-arrestin2 in complex with Fab30
    • Complex: beta-arrestin2
      • Protein or peptide: Beta-arrestin-2Arrestin beta 2
    • Complex: Fab30
      • Protein or peptide: Fab30 Heavy Chain
      • Protein or peptide: Fab30 Light Chain
    • Complex: Vasopressin V2 receptorVasopressin receptor 2
      • Protein or peptide: Vasopressin V2 receptorVasopressin receptor 2
Function / homology
Function and homology information


renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / angiotensin receptor binding / desensitization of G protein-coupled receptor signaling pathway / positive regulation of systemic arterial blood pressure / hemostasis / telencephalon development ...renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / angiotensin receptor binding / desensitization of G protein-coupled receptor signaling pathway / positive regulation of systemic arterial blood pressure / hemostasis / telencephalon development / inositol hexakisphosphate binding / G protein-coupled receptor internalization / positive regulation of intracellular signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / endocytic vesicle / positive regulation of vasoconstriction / clathrin-coated pit / cellular response to hormone stimulus / activation of adenylate cyclase activity / phosphatidylinositol binding / response to cytokine / peptide binding / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / receptor internalization / Vasopressin regulates renal water homeostasis via Aquaporins / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / G alpha (s) signalling events / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / endosome / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / signal transduction / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain ...Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin E-set
Similarity search - Domain/homology
Vasopressin V2 receptor / Beta-arrestin-2
Similarity search - Component
Biological speciesBos taurus (cattle) / Mus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsMaharana J / Sarma P / Yadav MK / Banerjee R / Shukla AK
Funding support India, 1 items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)IPA/2020/000405 India
CitationJournal: Mol.Cell / Year: 2023
Title: Structure of beta-arrestin in complex with a phosphopeptide
Authors: Maharana J / Sarma P / Yadav MK / Banerjee R / Shukla AK
History
DepositionAug 24, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34175.png

Downloads & links

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Map

FileDownload / File: emd_34175.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map with pixel size 0.82.
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.31890556 - 0.49505275
Average (Standard dev.)0.00029509788 (±0.009845081)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A with pixel size 0.82.

Fileemd_34175_half_map_1.map
AnnotationHalf map A with pixel size 0.82.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B with pixel size 0.82.

Fileemd_34175_half_map_2.map
AnnotationHalf map B with pixel size 0.82.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Peptide3 bound beta-arrestin2 in complex with Fab30

EntireName: Peptide3 bound beta-arrestin2 in complex with Fab30
Components
  • Complex: Peptide3 bound beta-arrestin2 in complex with Fab30
    • Complex: beta-arrestin2
      • Protein or peptide: Beta-arrestin-2Arrestin beta 2
    • Complex: Fab30
      • Protein or peptide: Fab30 Heavy Chain
      • Protein or peptide: Fab30 Light Chain
    • Complex: Vasopressin V2 receptorVasopressin receptor 2
      • Protein or peptide: Vasopressin V2 receptorVasopressin receptor 2

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Supramolecule #1: Peptide3 bound beta-arrestin2 in complex with Fab30

SupramoleculeName: Peptide3 bound beta-arrestin2 in complex with Fab30 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 280 KDa

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Supramolecule #2: beta-arrestin2

SupramoleculeName: beta-arrestin2 / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (cattle)

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Supramolecule #3: Fab30

SupramoleculeName: Fab30 / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: Vasopressin V2 receptor

SupramoleculeName: Vasopressin V2 receptor / type: complex / ID: 4 / Chimera: Yes / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Beta-arrestin-2

MacromoleculeName: Beta-arrestin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 47.217676 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGEKPGTRVF KKSSPNGKLT VYLGKRDFVD HLDKVDPVDG VVLVDPDYLK DRKVFVTLTV AFRYGREDCD VLGLSFRKDL FIANYQAFP PTPNPPRPPT RLQERLLRKL GQHAHPFFFT IPQNLPSSVT LQPGPEDTGK ALGVDFEIRA FVAKSLEEKS H KRNSVRLV ...String:
MGEKPGTRVF KKSSPNGKLT VYLGKRDFVD HLDKVDPVDG VVLVDPDYLK DRKVFVTLTV AFRYGREDCD VLGLSFRKDL FIANYQAFP PTPNPPRPPT RLQERLLRKL GQHAHPFFFT IPQNLPSSVT LQPGPEDTGK ALGVDFEIRA FVAKSLEEKS H KRNSVRLV IRKVQFAPEK PGPQPSAETT RHFLMSDRSL HLEASLDKEL YYHGEPLNVN VHVTNNSTKT VKKIKVSVRQ YA DIVLFST AQYKVPVAQV EQDDQVSPSS TFSKVYTITP FLANNREKRG LALDGKLKHE DTNLASSTIV KEGANKEVLG ILV SYRVKV KLVVSRGGDV SVELPFVLMH PKPHDHIALP RPQSAATHPP TLLPSAVPET DAPVDTNLIE FETNYATDDD IVFE DFARL RLKGLKDEDY DDQFC

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Macromolecule #2: Fab30 Heavy Chain

MacromoleculeName: Fab30 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.512354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THHHHHHHH

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Macromolecule #3: Fab30 Light Chain

MacromoleculeName: Fab30 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: Vasopressin V2 receptor

MacromoleculeName: Vasopressin V2 receptor / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.790874 KDa
SequenceString:
ARGR(TPO)PP(SEP)LG PQDE(SEP)C(TPO)(TPO)A(SEP) (SEP)(SEP)LAKD(TPO)(SEP)(SEP)

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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

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
300.0 mMNaClSodium chlorideSodium chloride
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP / Details: Blotted for 3 seconds before plunging..

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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: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 9720 / Average electron dose: 48.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2444407
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5tv1

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 18492

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Atomic model buiding 1

Initial modelPDB ID:

5tv1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8goc:
Structure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human Vasopressin V2 receptor, V2R

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