[English] 日本語
Yorodumi
- PDB-1cf1: ARRESTIN FROM BOVINE ROD OUTER SEGMENTS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cf1
TitleARRESTIN FROM BOVINE ROD OUTER SEGMENTS
ComponentsPROTEIN (ARRESTIN)
KeywordsSTRUCTURAL PROTEIN / VISUAL ARRESTIN / DESENSITISATION OF THE VISUAL TRANSDUCTION CASCADE / BINDING TO ACTICATED AND PHOSPHORYLATED RHODOPSIN
Function / homology
Function and homology information


opsin binding / Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / phosphoprotein binding / G protein-coupled receptor binding / signal transduction / identical protein binding ...opsin binding / Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / phosphoprotein binding / G protein-coupled receptor binding / signal transduction / identical protein binding / membrane / cytosol
Similarity search - Function
Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / 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 ...Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsHirsch, J.A. / Schubert, C. / Gurevich, V.V. / Sigler, P.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: The 2.8 A crystal structure of visual arrestin: a model for arrestin's regulation.
Authors: Hirsch, J.A. / Schubert, C. / Gurevich, V.V. / Sigler, P.B.
History
DepositionMar 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (ARRESTIN)
B: PROTEIN (ARRESTIN)
C: PROTEIN (ARRESTIN)
D: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)181,0434
Polymers181,0434
Non-polymers00
Water45025
1
A: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)45,2611
Polymers45,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)45,2611
Polymers45,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)45,2611
Polymers45,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)45,2611
Polymers45,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: PROTEIN (ARRESTIN)

D: PROTEIN (ARRESTIN)


Theoretical massNumber of molelcules
Total (without water)90,5212
Polymers90,5212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area2200 Å2
ΔGint-5 kcal/mol
Surface area34700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.850, 193.190, 191.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.07517, -0.046137, -0.996103), (-0.040167, -0.998258, 0.043206), (-0.996361, 0.036763, -0.076892)
Vector: 144.60181, 71.9865, 152.9706)

-
Components

#1: Protein
PROTEIN (ARRESTIN) / RETINAL S-ANTIGEN / 48 KD PROTEIN


Mass: 45260.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: RETINA / Cell: ROD OUTER SEGMENTS / Cellular location: CYTOPLASM / Organ: EYE / Plasmid: PTRC / Production host: Escherichia coli (E. coli) / Strain (production host): ER2508 / References: UniProt: P08168
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71 % / Description: BEAMLINES: APS, 19ID
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: used microseeding / PH range low: 8.8 / PH range high: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMTris-HCl1reservoir
2200 mMammonium acetate1reservoir
322-25 %isopropanol1reservoir
410 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.00523
DetectorType: ADSC / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00523 Å / Relative weight: 1
ReflectionResolution: 2.8→60 Å / Num. obs: 242164 / % possible obs: 84.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 154.9 Å2 / Rsym value: 0.051 / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.342 / % possible all: 42

-
Processing

Software
NameClassification
SHARPphasing
CNSrefinement
PHASESphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→45 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 7316256.45 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1762 2.5 %RANDOM
Rwork0.233 ---
obs0.233 69807 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.45 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 59.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.4 Å20 Å20 Å2
2--6.98 Å20 Å2
3----2.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11675 0 0 25 11700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.441.5
X-RAY DIFFRACTIONc_mcangle_it5.622
X-RAY DIFFRACTIONc_scbond_it5.452
X-RAY DIFFRACTIONc_scangle_it7.972.5
Refine LS restraints NCSNCS model details: CONSTR / Weight Biso : 2 / Weight position: 300
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.456 187 2.8 %
Rwork0.44 6520 -
obs--52.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 45 Å / σ(F): 0 / % reflection Rfree: 2.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.456 / % reflection Rfree: 2.8 % / Rfactor Rwork: 0.44

+
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