[English] 日本語
Yorodumi
- PDB-3c2h: Crystal Structure of SYS-1 at 2.6A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c2h
TitleCrystal Structure of SYS-1 at 2.6A resolution
ComponentsSys-1 protein
KeywordsCELL ADHESION / SYS-1 / Caenorhabditis elegans / beta-catenin / WNT
Function / homology
Function and homology information


polarity specification of proximal/distal axis / gonad morphogenesis / positive regulation of mesodermal cell fate specification / mesodermal cell fate specification / regulation of asymmetric cell division / gonad development / endodermal cell fate commitment / proximal/distal pattern formation / embryonic digestive tract development / embryo development ending in birth or egg hatching ...polarity specification of proximal/distal axis / gonad morphogenesis / positive regulation of mesodermal cell fate specification / mesodermal cell fate specification / regulation of asymmetric cell division / gonad development / endodermal cell fate commitment / proximal/distal pattern formation / embryonic digestive tract development / embryo development ending in birth or egg hatching / female gonad development / kinetochore / Wnt signaling pathway / male gonad development / scaffold protein binding / cell cortex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Sys-1 C-terminal domain-like / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / Beta-catenin homolog sys-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsLiu, J. / Phillips, B.T. / Amaya, M.F. / Kimble, J. / Xu, W.
Citation
Journal: Dev.Cell / Year: 2008
Title: The C. elegans SYS-1 protein is a bona fide beta-catenin.
Authors: Liu, J. / Phillips, B.T. / Amaya, M.F. / Kimble, J. / Xu, W.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2005
Title: A beta-catenin identified by functional rather than sequence criteria and its role in Wnt/MAPK signaling.
Authors: Miskowski, J. / Li, Y. / Kimble, J.
#2: Journal: Dev.Biol. / Year: 2001
Title: The sys-1 gene and sexual dimorphism during gonadogenesis in Caenorhabditis elegans.
Authors: Kidd III, A.R. / Miskowski, J.A. / Siegfried, K.R. / Sawa, H. / Kimble, J.
#3: Journal: Genetics / Year: 2004
Title: The sys-1 and sys-3 genes cooperate with Wnt signaling to establish the proximal-distal axis of the Caenorhabditis elegans gonad.
Authors: Phillips, B.T. / Kidd III, A.R. / King, R. / Hardin, J. / Kimble, J.
#4: Journal: Development / Year: 2007
Title: Binary cell fate specification during C. elegans embryogenesis driven by reiterated reciprocal asymmetry of TCF POP-1 and its coactivator beta-catenin SYS-1.
Authors: Huang, S. / Shetty, P. / Robertson, S.M. / Lin, R.
History
DepositionJan 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sys-1 protein
B: Sys-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4247
Polymers141,8672
Non-polymers5575
Water70339
1
A: Sys-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3074
Polymers70,9331
Non-polymers3733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sys-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1183
Polymers70,9331
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)203.500, 95.048, 149.390
Angle α, β, γ (deg.)90.000, 124.710, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALAAA180 - 2191 - 40
21METMETALAALABB180 - 2191 - 40
32ASNASNMETMETAA225 - 59046 - 411
42ASNASNMETMETBB225 - 59046 - 411
53LYSLYSCYSCYSAA600 - 628421 - 449
63LYSLYSCYSCYSBB600 - 628421 - 449
74METMETLEULEUAA631 - 734452 - 555
84METMETLEULEUBB631 - 734452 - 555
95PROPROLEULEUAA742 - 792563 - 613
105PROPROLEULEUBB742 - 792563 - 613

-
Components

#1: Protein Sys-1 protein


Mass: 70933.336 Da / Num. of mol.: 2 / Fragment: Armadillor Domain (UNP residues 180 - 798)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sys-1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9XVI2
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 4.19 Å3/Da / Density % sol: 70.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Hepes, 0.6 M Na/K Tartrate, 20 mM Glycine and 5mM DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 70425 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Χ2: 1.155 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.437 / Num. unique all: 6527 / Χ2: 1.033 / % possible all: 91.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.56 Å
Translation2.5 Å49.56 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.57 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.065 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.391 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 3573 5.1 %RANDOM
Rwork0.245 ---
all0.2466 72547 --
obs0.247 70332 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.547 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å20.12 Å2
2--0.34 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9770 0 37 39 9846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210026
X-RAY DIFFRACTIONr_angle_refined_deg1.141.96713646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.00351231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.89224.279437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85151716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8271559
X-RAY DIFFRACTIONr_chiral_restr0.0880.21584
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027501
X-RAY DIFFRACTIONr_nbd_refined0.2060.24735
X-RAY DIFFRACTIONr_nbtor_refined0.3060.27024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.210
X-RAY DIFFRACTIONr_mcbond_it0.90726386
X-RAY DIFFRACTIONr_mcangle_it1.655310115
X-RAY DIFFRACTIONr_scbond_it1.84344082
X-RAY DIFFRACTIONr_scangle_it2.96463531
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3282 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.265
LOOSE THERMAL1.4210
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 239 -
Rwork0.333 4516 -
all-4755 -
obs--90.26 %

+
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