[English] 日本語
Yorodumi
- PDB-7dfc: Crystal of Arrestin2-V2Rpp-3-Fab30 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dfc
TitleCrystal of Arrestin2-V2Rpp-3-Fab30 complex
Components
  • Beta-arrestin-1Arrestin
  • FAB30 HEAVY CHAIN
  • FAB30 LIGHT CHAIN
  • V2Rpp-3
KeywordsSIGNALING PROTEIN / Arrestin / G-protein-coupled receptor / Phosphopeptide / Antibody fragment
Function / homology
Function and homology information


MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / clathrin heavy chain binding / clathrin coat of coated pit / Ub-specific processing proteases / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis ...MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / clathrin heavy chain binding / clathrin coat of coated pit / Ub-specific processing proteases / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / inositol hexakisphosphate binding / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / G protein-coupled receptor internalization / acetylcholine receptor binding / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / clathrin binding / negative regulation of Notch signaling pathway / pseudopodium / phosphatidylinositol-3,4,5-trisphosphate binding / small molecule binding / positive regulation of receptor internalization / visual perception / G protein-coupled receptor binding / receptor internalization / protein transport / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / positive regulation of protein phosphorylation / signal transduction / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
Mus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsSun, J.P. / Yu, X. / Xiao, P. / He, Q.T. / Lin, J.Y. / Zhu, Z.L.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Nat Commun / Year: 2021
Title: Structural studies of phosphorylation-dependent interactions between the V2R receptor and arrestin-2.
Authors: He, Q.T. / Xiao, P. / Huang, S.M. / Jia, Y.L. / Zhu, Z.L. / Lin, J.Y. / Yang, F. / Tao, X.N. / Zhao, R.J. / Gao, F.Y. / Niu, X.G. / Xiao, K.H. / Wang, J. / Jin, C. / Sun, J.P. / Yu, X.
History
DepositionNov 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-arrestin-1
V: V2Rpp-3
L: FAB30 LIGHT CHAIN
H: FAB30 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8275
Polymers102,7354
Non-polymers921
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-63 kcal/mol
Surface area36180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.137, 122.653, 144.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

-
Components

-
Antibody , 2 types, 2 molecules LH

#3: Antibody FAB30 LIGHT CHAIN


Mass: 24751.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#4: Antibody FAB30 HEAVY CHAIN


Mass: 26828.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

-
Protein / Protein/peptide , 2 types, 2 molecules AV

#1: Protein Beta-arrestin-1 / Arrestin / Arrestin beta-1 / Arrestin-2


Mass: 48272.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ARRB1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P17870
#2: Protein/peptide V2Rpp-3


Mass: 2881.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 2 types, 58 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.5 / Details: 15% PEG 3350, 0.1M HEPES, 0.2mM DMSO

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.05 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.45→46.69 Å / Num. obs: 38166 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 60.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Net I/σ(I): 18.5
Reflection shellResolution: 2.45→2.55 Å / Rmerge(I) obs: 0.959 / Num. unique obs: 4165 / CC1/2: 0.85 / Rpim(I) all: 0.548

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JQI

4jqi


Resolution: 2.49→46.69 Å / SU ML: 0.3759 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.3846 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.284 1892 5.2 %
Rwork0.2285 34493 -
obs0.2315 36385 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.3 Å2
Refinement stepCycle: LAST / Resolution: 2.49→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5915 0 6 57 5978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916053
X-RAY DIFFRACTIONf_angle_d1.15888271
X-RAY DIFFRACTIONf_chiral_restr0.0679963
X-RAY DIFFRACTIONf_plane_restr0.00731053
X-RAY DIFFRACTIONf_dihedral_angle_d21.26852141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.41241400.33842388X-RAY DIFFRACTION98.63
2.55-2.620.34681420.31332407X-RAY DIFFRACTION99.07
2.62-2.690.35241220.29082459X-RAY DIFFRACTION99.69
2.69-2.780.30991490.26992443X-RAY DIFFRACTION99.69
2.78-2.880.34311280.27222421X-RAY DIFFRACTION99.61
2.88-30.44521160.28372491X-RAY DIFFRACTION99.69
3-3.130.33671370.28412422X-RAY DIFFRACTION99.77
3.13-3.30.35551200.2692480X-RAY DIFFRACTION99.88
3.3-3.50.3431300.25432463X-RAY DIFFRACTION99.81
3.5-3.770.31921410.24012448X-RAY DIFFRACTION99.81
3.77-4.150.30921140.22112506X-RAY DIFFRACTION99.81
4.15-4.750.21921520.17922475X-RAY DIFFRACTION99.85
4.75-5.990.22351600.19582494X-RAY DIFFRACTION99.89
5.99-46.70.25221410.20552596X-RAY DIFFRACTION98.63
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1931586594-0.8254051944410.7925828629533.55146647409-0.6571395279610.5485576505310.1510739397810.3457190788180.19468864573-0.190718663934-0.422554619324-0.38359398518-1.330097495790.02346055002250.2524014361091.386705817630.2792853398340.08946746851670.4737517285320.1527984297090.54107913205612.797556138621.0803231625-1.87527395642
21.61337267145-0.8592661830450.5544464442910.661726398767-0.9903155132263.953890384120.01030432109290.1516086003730.3816731582470.0901110010112-0.330317183599-0.517896295763-1.400553103630.7008957656220.2605643822311.286418882920.02133122920880.05304586332980.415368377790.1765992221530.69537020423321.325360107920.3507748391-4.57838821484
32.04314914977-1.818368418920.2435966370595.23186959577-1.481238629381.001196767810.2072694254420.2355952099210.5003366730680.243053911956-0.533750998115-0.0995469373724-1.22499858705-0.1734351713660.2246684875291.429263824360.254448505359-0.02271434779470.46741948241-0.005774983622370.48977354741311.179611702817.24503640883.99353380436
41.6113041005-0.305266368195-1.251737495812.42249805243-2.00104622575.68544054625-0.00845852986977-0.0145184601544-0.2422667328940.644352060605-0.341697052757-0.01314022071710.737852562912-0.5314320351620.3207230831230.842620796038-0.06470352570360.006329889313580.361649568411-0.04958784929810.3747267547186.74648549945-12.762479728425.9568873003
52.799921230970.861021723381-1.600303060325.17896372296-2.643563816126.002458002460.1723261252280.4498182385480.212310033431-0.0260443722174-0.324433147424-0.111577508634-0.797206904523-0.4011803500740.1649223605240.6221158580730.10810068518-0.009597802613510.307297734432-0.06249432961910.2599674186365.848078802432.4569085336714.4743433534
63.412639001580.206718290675-1.192647176152.601238773151.656986934051.430897039050.04790316308610.4961419803860.08129314063970.0194370809997-0.3338489505270.0265603905266-0.16063164842-0.4230600842720.1632170987680.562738295829-0.009810791825990.0267889775970.252580427121-0.06198717882660.3822323543436.84859334652-5.307812629118.2216862579
73.6416862248-3.41048376656-3.39439498855.472698081975.462105269965.297328127660.04883427142620.472686989880.0997503566478-0.198285953542-0.7106479923720.393505386311-0.93029307854-0.4313419871130.4359372987491.370740188330.2841722301880.02331894685240.7085619620690.09900709893850.5098929362476.3756050835421.4046388854-4.35323057045
81.322068831030.9493417244551.221783474551.354886686670.7156718787721.36939390945-0.5506033517420.95987723298-0.14555849015-0.5174046937490.419890177779-0.4770050564870.021768709948-1.538738535250.01743451295040.975626136342-0.07720652583110.2218217220311.65659890899-0.2053501185620.383531807138-1.36957839326-5.02559494337-24.1722926032
95.385338880361.21407815417-0.5892474352453.248855121171.201904075228.90193017325-0.8459746179491.15082791015-0.367186095858-0.7593004450880.2902131132320.22438515582-0.0863114335331-0.03607489639240.5502511997510.99852272537-0.2040979404870.05613027143760.675610128588-0.08460112448610.574521217615-26.133464601-22.7436829783-41.3588985852
101.073968891561.055885527211.381856400451.864904815581.077053384352.48180551949-0.269415094840.895485006769-0.588527978086-0.2885736456640.247260923625-0.4335207534970.142300060563-2.44850844383-0.1600968006520.771095298285-0.0129776097124-0.01322064581392.52084270128-0.1590034879460.0139613269841-15.5510934041-8.45940430583-4.16916873042
112.779162639262.071734066463.575799677091.847249663192.402703325033.671268569930.498603871297-1.01169389542-0.4898131718760.0940097433269-0.27589541913-0.1332543329760.733869172522-1.04724804644-0.2042252913760.957221904808-0.0629651713106-0.01590918528671.54780074516-0.08795382342390.521498061349-15.5447482794-17.4390828913-16.9568021857
124.28361804650.1261206747721.707873589650.518293495693-1.740886329157.078458225560.486904643944-2.16066137532-1.78702810257-0.687410428114-0.321532972606-0.6501116311861.15618470434-0.141060842616-0.1533598515831.2103082861-0.2696141589730.0944266175321.065465391550.1540560909771.02405281222-22.1463250836-31.2601740432-27.1929827106
135.68064289169-0.4585751169596.529465687178.89763316168-3.02966556278.222622884760.469928905059-1.18351897004-0.5498723870621.51533947488-0.1692937419790.3078456753790.5417874315840.706587253955-0.3021863716631.03839260808-0.1699948461840.05858111560011.18595762191-0.06265685277550.544764519942-23.728261894-30.1542894238-27.5930599127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 274 )
5X-RAY DIFFRACTION5chain 'A' and (resid 275 through 329 )
6X-RAY DIFFRACTION6chain 'A' and (resid 330 through 367 )
7X-RAY DIFFRACTION7chain 'V' and (resid 346 through 367 )
8X-RAY DIFFRACTION8chain 'L' and (resid 14 through 126 )
9X-RAY DIFFRACTION9chain 'L' and (resid 127 through 224 )
10X-RAY DIFFRACTION10chain 'H' and (resid 17 through 106 )
11X-RAY DIFFRACTION11chain 'H' and (resid 107 through 156 )
12X-RAY DIFFRACTION12chain 'H' and (resid 157 through 184 )
13X-RAY DIFFRACTION13chain 'H' and (resid 185 through 234 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more