[English] 日本語
Yorodumi
- PDB-9etn: Crystal structure of murine CRTAC1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9etn
TitleCrystal structure of murine CRTAC1
ComponentsCartilage acidic protein 1
KeywordsSIGNALING PROTEIN / beta-propeller / potassium binding / calcium binding
Function / homology
Function and homology information


olfactory bulb development / axonal fasciculation / regulation of synapse assembly / growth cone / postsynaptic density / calcium ion binding / glutamatergic synapse / extracellular region
Similarity search - Function
ASPIC/UnbV / Cartilage acidic protein 1 / ASPIC and UnbV / FG-GAP-like repeat / : / Calcium-binding EGF domain / FG-GAP repeat / Integrin alpha, N-terminal / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. ...ASPIC/UnbV / Cartilage acidic protein 1 / ASPIC and UnbV / FG-GAP-like repeat / : / Calcium-binding EGF domain / FG-GAP repeat / Integrin alpha, N-terminal / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain
Similarity search - Domain/homology
: / Cartilage acidic protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.584 Å
AuthorsBeugelink, J.W. / Hof, H. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: J.Mol.Biol. / Year: 2024
Title: CRTAC1 has a Compact beta-propeller-TTR Core Stabilized by Potassium Ions.
Authors: Beugelink, J.W. / Hof, H. / Janssen, B.J.C.
History
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cartilage acidic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,10912
Polymers64,1581
Non-polymers95111
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-13 kcal/mol
Surface area20940 Å2
Unit cell
Length a, b, c (Å)167.514, 84.204, 59.718
Angle α, β, γ (deg.)90.000, 102.702, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-978-

HOH

21A-1100-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Cartilage acidic protein 1 / 68 kDa chondrocyte-expressed protein / CEP-68 / ASPIC / Protein CRTAC1-B


Mass: 64157.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crtac1, Aspic1, Cep68 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8R555
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 324 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM sodium-malonate pH 5.0, 12% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6702 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6702 Å / Relative weight: 1
ReflectionResolution: 1.582→81.707 Å / Num. obs: 54952 / % possible obs: 86.5 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.042 / Rrim(I) all: 0.099 / Net I/σ(I): 10.9
Reflection shellResolution: 1.582→1.786 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.777 / Num. unique obs: 2748 / CC1/2: 0.667 / Rpim(I) all: 0.409 / Rrim(I) all: 0.885 / % possible all: 67.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.584→81.707 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.149 / Average fsc free: 0.9742 / Average fsc work: 0.9849 / Cross valid method: FREE R-VALUE / ESU R: 0.2 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1946 2798 5.092 %
Rwork0.1501 52152 -
all0.152 --
obs-54950 49.996 %
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: 24.695 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0.569 Å2
2---1.047 Å2-0 Å2
3---1.927 Å2
Refinement stepCycle: LAST / Resolution: 1.584→81.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 0 48 314 4593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124380
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163962
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.6565955
X-RAY DIFFRACTIONr_angle_other_deg0.7251.5819101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6025563
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg0.022202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.703538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72310.09666
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.61810222
X-RAY DIFFRACTIONr_chiral_restr0.060.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025364
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021079
X-RAY DIFFRACTIONr_nbd_refined0.2340.2800
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.23868
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22179
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2309
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.236
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.29
X-RAY DIFFRACTIONr_nbd_other0.2050.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.215
X-RAY DIFFRACTIONr_mcbond_it1.4652.4662206
X-RAY DIFFRACTIONr_mcbond_other1.4512.4662206
X-RAY DIFFRACTIONr_mcangle_it2.1854.4282755
X-RAY DIFFRACTIONr_mcangle_other2.1864.4292756
X-RAY DIFFRACTIONr_scbond_it1.6412.7922174
X-RAY DIFFRACTIONr_scbond_other1.642.7932175
X-RAY DIFFRACTIONr_scangle_it2.4024.9993198
X-RAY DIFFRACTIONr_scangle_other2.40253199
X-RAY DIFFRACTIONr_lrange_it3.72924.4624874
X-RAY DIFFRACTIONr_lrange_other3.47424.2654804
X-RAY DIFFRACTIONr_rigid_bond_restr2.83438342
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
1.584-1.6250.30650.2391050.24281140.9740.9461.35570.232
1.625-1.6690.297220.2224140.22678610.9390.9645.54640.215
1.669-1.7180.294310.2257330.22876700.9460.9679.96090.219
1.718-1.770.247470.21410370.21574610.9680.97114.52890.205
1.77-1.8280.256630.20513550.20772230.9640.97619.63170.193
1.828-1.8930.229720.19811660.269550.9640.97717.80010.179
1.893-1.9640.224770.17516700.17767780.9650.98225.77460.147
1.964-2.0440.2151850.17535640.17765160.9730.98257.53530.147
2.044-2.1350.212130.16440150.16662610.9720.98567.52910.136
2.135-2.2390.212290.15939110.16259600.9740.98669.46310.13
2.239-2.360.2091850.14936390.15256600.9750.98767.56180.121
2.36-2.5030.2052450.15349490.15653710.9780.98796.70450.126
2.503-2.6760.2132620.14947780.15250450.9750.98899.90090.127
2.676-2.890.2022370.14544590.14847000.9760.98899.91490.131
2.89-3.1650.2052420.1540930.15343450.9690.98799.76990.143
3.165-3.5380.1842050.1537190.15239280.980.98799.89820.149
3.538-4.0840.1811320.13623580.13834830.9820.9971.49010.144
4.084-4.9990.1411610.11627910.11829540.990.99399.93230.133
4.999-7.0570.1961250.15821530.1622850.9790.98899.69370.178
7.057-81.7070.216600.18312430.18413080.9540.96299.61770.226

+
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