[English] 日本語
Yorodumi
- PDB-6wsk: Crystal Structure of the Cannabinoid Receptor 1 Interacting Prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wsk
TitleCrystal Structure of the Cannabinoid Receptor 1 Interacting Protein 1a (CRIP1a)
ComponentsEndolysin,CB1 cannabinoid receptor-interacting protein 1 fusion
KeywordsSIGNALING PROTEIN / beta barrel / cargo carrier
Function / homology
Function and homology information


type 1 cannabinoid receptor binding / : / negative regulation of signaling receptor activity / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium ...type 1 cannabinoid receptor binding / : / negative regulation of signaling receptor activity / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / plasma membrane / cytoplasm
Similarity search - Function
CB1 cannabinoid receptor-interacting protein 1 / CB1 cannabinoid receptor-interacting protein 1 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Endolysin / CB1 cannabinoid receptor-interacting protein 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBooth, W.T. / Howlett, A.C. / Lowther, W.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA042157 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Cannabinoid receptor interacting protein 1a interacts with myristoylated G alpha i N terminus via a unique gapped beta-barrel structure.
Authors: Booth, W.T. / Clodfelter, J.E. / Leone-Kabler, S. / Hughes, E.K. / Eldeeb, K. / Howlett, A.C. / Lowther, W.T.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endolysin,CB1 cannabinoid receptor-interacting protein 1 fusion


Theoretical massNumber of molelcules
Total (without water)39,2151
Polymers39,2151
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, This protein purifies as a monomer on a Superdex 75 column
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.177, 68.177, 146.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Endolysin,CB1 cannabinoid receptor-interacting protein 1 fusion / Lysis protein / Lysozyme / Muramidase / CRIP-1


Mass: 39214.863 Da / Num. of mol.: 1 / Mutation: E11Q, D20N, C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Cnrip1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P00720, UniProt: Q5M7A7, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30 mg/mL, 0.1 M sodium citrate (pH 4-5.5), and 0.3-0.6 ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.55→19.86 Å / Num. obs: 50935 / % possible obs: 99.8 % / Redundancy: 20.1 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.01 / Rrim(I) all: 0.06 / Net I/σ(I): 28.4
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 2 / Num. unique obs: 4957 / CC1/2: 0.75 / Rpim(I) all: 0.37 / Rrim(I) all: 1.31 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.14_3260refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fa0

3fa0


Resolution: 1.55→19.86 Å / SU ML: 0.1649 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3983
RfactorNum. reflection% reflection
Rfree0.2245 1689 3.32 %
Rwork0.2064 --
obs0.207 50933 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.43 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 0 217 2525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992386
X-RAY DIFFRACTIONf_angle_d1.09713232
X-RAY DIFFRACTIONf_chiral_restr0.0604363
X-RAY DIFFRACTIONf_plane_restr0.0076408
X-RAY DIFFRACTIONf_dihedral_angle_d2.57852004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.28871360.26613985X-RAY DIFFRACTION99.21
1.6-1.650.2561380.24344028X-RAY DIFFRACTION99.57
1.65-1.710.28541390.23374040X-RAY DIFFRACTION99.67
1.71-1.770.25641380.23254022X-RAY DIFFRACTION99.86
1.77-1.850.25241400.22444077X-RAY DIFFRACTION100
1.85-1.950.25361390.22064064X-RAY DIFFRACTION100
1.95-2.070.22861390.21294065X-RAY DIFFRACTION100
2.07-2.230.23671410.20054087X-RAY DIFFRACTION100
2.23-2.460.20961400.20094122X-RAY DIFFRACTION100
2.46-2.810.25141420.20584138X-RAY DIFFRACTION100
2.81-3.540.20461440.20344198X-RAY DIFFRACTION100
3.54-19.730.20361530.19384418X-RAY DIFFRACTION99.98
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)
12.27639340577-0.429946169091-0.4525751876465.77862419451-0.147190942153.354168740980.0777498866555-0.03428380293960.002481334341570.07902011615410.04399888733570.0718847160595-0.164462697960.0172065375346-0.1530609872060.109314973799-0.05728357589310.02849121025870.219653024207-0.0009922934338540.12695650983339.02532026517.444796475367.7050928703
21.97859840886-1.161898734670.95277598934.0797292159-2.609424086414.245431888760.0802461823686-0.072404148163-0.104937918459-0.0192585861777-0.1066225140680.06901061158240.1075256883920.1987091552770.07218850310780.1053855330840.007704393464060.04297949249990.209473174366-0.004784952839190.13681844355243.030872120616.769295071159.3422407966
30.1338913710560.0832560832640.07344369683630.312585726579-0.1739379109030.2210675637760.0409848158537-0.1025937208490.00713818793956-0.106004968389-0.0636176574060.005648066587950.02619406346010.05248875161120.02627991798710.245193860822-0.002203380170530.005243224296850.2537451767790.04033562244820.26896289849147.428110813221.729186411951.5547373701
40.231500173276-0.02193880397340.2355751920870.2942087557880.07721874902760.547657800480.0876250007376-0.02673339925230.008056537141090.0441733313216-0.0728067115125-0.0176921856842-0.0161748780843-0.0885866691116-0.01659879213570.279333196650.00897415898446-0.005443917053860.281323248482-0.006777175725620.29903879491845.853435768225.536836461148.0704688232
50.3284405645670.04641371046910.1949356068050.570905063492-0.007429549820540.1152244418490.0854261819742-0.0331416180825-0.0895972479795-0.00512651245182-0.0277705503582-0.0298963419593-0.0032479099496-0.0350325957234-0.0671613177280.3288198364870.02016258281170.008010494938890.3307978557410.009440118107240.29843991535750.009628126927.881460810547.671155986
60.715363604158-0.4541078628390.1097887028390.4605840608560.2180561078680.487911157941-0.0490340633419-0.133177360539-0.0002780429732040.1491729740790.0528990090468-0.01699658000090.100815898135-0.1094458614660.03527160395530.335432045621-0.075092228679-0.006702382694860.297769441721-0.01463499333570.28158702019945.612645744824.148104259156.9154078834
70.18059109308-0.2614456297410.07805801698150.6162088353290.159315051750.7184371229460.04097651883070.03139601955570.00606837167305-0.0426627470355-0.1568468068240.00954263470672-0.065809130309-0.1159315075590.1400922715770.355125692221-0.06817857137410.03744303051390.343678420805-0.009868955344090.35640318274748.48163726826.203624286149.4846060988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -165 through -85 )
2X-RAY DIFFRACTION2chain 'A' and (resid -84 through -1 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 16 )
4X-RAY DIFFRACTION4chain 'A' and (resid 17 through 53 )
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 115 )
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 134 )
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 164 )

+
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