[English] 日本語
Yorodumi
- PDB-6d32: Crystal structure of Xenopus Smoothened in complex with cyclopamine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d32
TitleCrystal structure of Xenopus Smoothened in complex with cyclopamine
ComponentsSmoothened,Soluble cytochrome b562,Smoothened
KeywordsMEMBRANE PROTEIN / GPCR / Hedgehog signaling / Class Frizzled / Sterol
Function / homology
Function and homology information


tissue development / patched binding / pattern specification process / commissural neuron axon guidance / smoothened signaling pathway / membrane => GO:0016020 / central nervous system development / electron transport chain / G protein-coupled receptor activity / Wnt signaling pathway ...tissue development / patched binding / pattern specification process / commissural neuron axon guidance / smoothened signaling pathway / membrane => GO:0016020 / central nervous system development / electron transport chain / G protein-coupled receptor activity / Wnt signaling pathway / periplasmic space / electron transfer activity / cilium / iron ion binding / heme binding / dendrite / metal ion binding / plasma membrane
Similarity search - Function
Smoothened / Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled ...Smoothened / Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclopamine / Uncharacterized protein / Soluble cytochrome b562 / Protein smoothened
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.751 Å
AuthorsHuang, P. / Zheng, S. / Kim, Y. / Kruse, A.C. / Salic, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM110041 United States
CitationJournal: Cell / Year: 2018
Title: Structural Basis of Smoothened Activation in Hedgehog Signaling.
Authors: Huang, P. / Zheng, S. / Wierbowski, B.M. / Kim, Y. / Nedelcu, D. / Aravena, L. / Liu, J. / Kruse, A.C. / Salic, A.
History
DepositionApr 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Smoothened,Soluble cytochrome b562,Smoothened
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8083
Polymers68,9841
Non-polymers8232
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area29580 Å2
Unit cell
Length a, b, c (Å)145.778, 79.232, 104.076
Angle α, β, γ (deg.)90.000, 108.510, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Smoothened,Soluble cytochrome b562,Smoothened / Cytochrome b-562


Mass: 68984.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog), (gene. exp.) Escherichia coli (E. coli)
Gene: smo, Smo, cybC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q98SW5, UniProt: P0ABE7, UniProt: A0A1L8GTP2*PLUS
#2: Chemical ChemComp-CY8 / Cyclopamine / (3alpha,8alpha,14beta,22S,23R)-17,23-epoxyveratraman-3-ol


Mass: 411.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H41NO2
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.23 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 35-45% PEG 300, 300-500 mM LiSO4, 0.1 M MES pH 6-6.5

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0333 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 3.74→49.63 Å / Num. obs: 11676 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.992 / Net I/σ(I): 6.1
Reflection shellResolution: 3.74→3.81 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 504 / CC1/2: 0.617 / % possible all: 88.6

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L7D, 5KZY and 4O9R

5l7d

5kzy

4o9r


Resolution: 3.751→41.054 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 31.11
RfactorNum. reflection% reflection
Rfree0.26 587 5.12 %
Rwork0.227 --
obs0.2287 11455 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.84 Å2 / Biso mean: 90.0449 Å2 / Biso min: 40.22 Å2
Refinement stepCycle: final / Resolution: 3.751→41.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 60 0 4596
Biso mean--124.48 --
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034726
X-RAY DIFFRACTIONf_angle_d0.846418
X-RAY DIFFRACTIONf_chiral_restr0.028721
X-RAY DIFFRACTIONf_plane_restr0.003800
X-RAY DIFFRACTIONf_dihedral_angle_d14.3481715
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7506-4.12780.33921400.27522624276496
4.1278-4.72430.25271570.21582691284898
4.7243-5.94920.24311410.23472746288799
5.9492-41.05690.24371490.20922807295699

+
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