[English] 日本語
Yorodumi
- PDB-7q2t: Crystal structure of untagged rat C2orf32 (also known as CNRIP1) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q2t
TitleCrystal structure of untagged rat C2orf32 (also known as CNRIP1) in a domain-swapped conformation
ComponentsCB1 cannabinoid receptor-interacting protein 1
KeywordsPEPTIDE BINDING PROTEIN / Possible involvement in the cannabinoid system
Function / homologytype 1 cannabinoid receptor binding / CB1 cannabinoid receptor-interacting protein 1 / CB1 cannabinoid receptor-interacting protein 1 / : / negative regulation of signaling receptor activity / plasma membrane / cytoplasm / PHOSPHATE ION / CB1 cannabinoid receptor-interacting protein 1
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.651 Å
AuthorsSaul, L. / Steiner, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of untagged rat C2orf32 (also known as CNRIP1) in a domain-swapped conformation
Authors: Saul, L. / Steiner, R.A.
History
DepositionOct 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
XXX: CB1 cannabinoid receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7983
Polymers18,6801
Non-polymers1182
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, none
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-14 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.250, 79.600, 130.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11XXX-201-

NA

21XXX-382-

HOH

31XXX-420-

HOH

41XXX-486-

HOH

-
Components

#1: Protein CB1 cannabinoid receptor-interacting protein 1 / CRIP-1


Mass: 18680.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cnrip1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5M7A7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 5-10% PEG1500, SPG buffer pH 6.0-6.5, 5-10mM DTT

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.83 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 1.65→39.8 Å / Num. obs: 18699 / % possible obs: 99.2 % / Redundancy: 11.2 % / Biso Wilson estimate: 14.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.024 / Rrim(I) all: 0.081 / Net I/σ(I): 23
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.86 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 829 / CC1/2: 0.676 / Rpim(I) all: 0.325 / Rrim(I) all: 0.878 / % possible all: 90.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.651→39.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.227 / SU ML: 0.074 / Cross valid method: FREE R-VALUE / ESU R: 0.104 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.218 942 5.047 %
Rwork0.1677 17723 -
all0.17 --
obs-18665 99.008 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.047 Å2
Baniso -1Baniso -2Baniso -3
1--0.346 Å20 Å20 Å2
2--1.233 Å2-0 Å2
3----0.887 Å2
Refinement stepCycle: LAST / Resolution: 1.651→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 6 217 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131371
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151317
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.6551872
X-RAY DIFFRACTIONr_angle_other_deg1.3691.5783062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4735172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28822.87966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85215246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.238157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02302
X-RAY DIFFRACTIONr_nbd_refined0.1970.2190
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21129
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2594
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2620
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2134
X-RAY DIFFRACTIONr_metal_ion_refined0.10.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2830.223
X-RAY DIFFRACTIONr_nbd_other0.1670.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.238
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.10.21
X-RAY DIFFRACTIONr_mcbond_it1.7291.769661
X-RAY DIFFRACTIONr_mcbond_other1.7251.768660
X-RAY DIFFRACTIONr_mcangle_it2.622.636827
X-RAY DIFFRACTIONr_mcangle_other2.6212.637828
X-RAY DIFFRACTIONr_scbond_it2.1491.978710
X-RAY DIFFRACTIONr_scbond_other2.1471.978710
X-RAY DIFFRACTIONr_scangle_it3.3232.8791040
X-RAY DIFFRACTIONr_scangle_other3.3222.8791040
X-RAY DIFFRACTIONr_lrange_it5.41121.2251461
X-RAY DIFFRACTIONr_lrange_other5.4121.2361462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.651-1.6940.305600.26412110.26613960.8330.83691.04580.225
1.694-1.7410.305670.24112050.24413260.8920.88895.92760.197
1.741-1.7910.217630.21312100.21312730.9140.9171000.175
1.791-1.8460.184610.20212110.20112720.9290.9271000.163
1.846-1.9060.204580.19511580.19612160.940.9321000.156
1.906-1.9730.238670.18211190.18511860.9290.9361000.149
1.973-2.0470.227640.17810820.18111460.9350.9521000.15
2.047-2.1310.2580.16210550.16411130.9540.961000.134
2.131-2.2250.257540.15710030.16210580.930.95899.90550.138
2.225-2.3340.237550.1689460.17210010.9370.9481000.145
2.334-2.4590.241480.1629550.16610030.9310.9561000.141
2.459-2.6080.187510.1578520.1599030.9580.9631000.138
2.608-2.7870.158400.1478230.1478630.9690.9641000.129
2.787-3.0090.208420.1517840.1538260.9540.9641000.139
3.009-3.2940.231400.1527150.1567550.9390.9651000.145
3.294-3.680.157320.1546540.1546880.9690.97299.70930.154
3.68-4.2430.28210.1425950.1466160.950.971000.146
4.243-5.1820.186240.1275000.135240.9570.9781000.141
5.182-7.2680.214250.1994000.24250.9560.9561000.21
7.268-39.80.283120.2212450.2242610.8850.94898.46740.229

+
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