[English] 日本語
Yorodumi
- PDB-5v56: 2.9A XFEL structure of the multi-domain human smoothened receptor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v56
Title2.9A XFEL structure of the multi-domain human smoothened receptor (with E194M mutation) in complex with TC114
ComponentsSmoothened homolog,Flavodoxin,Smoothened homolog
KeywordsMEMBRANE PROTEIN / human smoothened receptor complex / GPCR Hedgehog signaling / GPCR / Class F / 7TM domain / hinge domain / extracellular cystein-rich domain / Flavodoxin / LCP / XFEL / TC114
Function / homology
Function and homology information


ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / response to inositol / regulation of heart morphogenesis / contact inhibition / negative regulation of hair follicle development / 9+0 non-motile cilium / regulation of somatic stem cell population maintenance / pancreas morphogenesis / epithelial-mesenchymal cell signaling ...ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / response to inositol / regulation of heart morphogenesis / contact inhibition / negative regulation of hair follicle development / 9+0 non-motile cilium / regulation of somatic stem cell population maintenance / pancreas morphogenesis / epithelial-mesenchymal cell signaling / myoblast migration / atrial septum morphogenesis / spinal cord dorsal/ventral patterning / determination of left/right asymmetry in lateral mesoderm / midgut development / left/right axis specification / patched binding / negative regulation of DNA binding / forebrain morphogenesis / somite development / type B pancreatic cell development / Activation of SMO / BBSome-mediated cargo-targeting to cilium / positive regulation of organ growth / smooth muscle tissue development / cerebellar cortex morphogenesis / mammary gland epithelial cell differentiation / cellular response to cholesterol / positive regulation of branching involved in ureteric bud morphogenesis / pattern specification process / commissural neuron axon guidance / dentate gyrus development / oxysterol binding / dopaminergic neuron differentiation / thalamus development / positive regulation of multicellular organism growth / positive regulation of smoothened signaling pathway / Class B/2 (Secretin family receptors) / cAMP-dependent protein kinase inhibitor activity / cell fate specification / central nervous system neuron differentiation / anterior/posterior pattern specification / positive regulation of mesenchymal cell proliferation / neural crest cell migration / dorsal/ventral neural tube patterning / hair follicle morphogenesis / ciliary membrane / smoothened signaling pathway / positive regulation of neuroblast proliferation / negative regulation of epithelial cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / heart looping / ciliary tip / protein kinase A catalytic subunit binding / odontogenesis of dentin-containing tooth / negative regulation of protein phosphorylation / neuroblast proliferation / vasculogenesis / Hedgehog 'off' state / skeletal muscle fiber development / astrocyte activation / centriole / homeostasis of number of cells within a tissue / protein sequestering activity / epithelial cell proliferation / central nervous system development / positive regulation of epithelial cell proliferation / Hedgehog 'on' state / positive regulation of protein import into nucleus / cerebral cortex development / G protein-coupled receptor activity / multicellular organism growth / protein import into nucleus / osteoblast differentiation / endocytic vesicle membrane / FMN binding / late endosome / gene expression / in utero embryonic development / electron transfer activity / cilium / protein stabilization / positive regulation of cell migration / intracellular membrane-bounded organelle / negative regulation of gene expression / apoptotic process / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / plasma membrane
Similarity search - Function
Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Flavodoxin, short chain / : / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein ...Smoothened, transmembrane domain / Smoothened, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Flavodoxin, short chain / : / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Flavodoxin, conserved site / Flavodoxin signature. / 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. / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-836 / FLAVIN MONONUCLEOTIDE / Flavodoxin / Protein smoothened
Similarity search - Component
Biological speciesHomo sapiens (human)
Desulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. ...Zhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. / Dharmarajan, V. / Griffin, P.R. / Gati, C. / Nelson, G. / Hunter, M.S. / Hanson, M.A. / Cherezov, V. / Stevens, R.C. / Tan, W. / Tao, H. / Xu, F.
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand.
Authors: Zhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. / Dharmarajan, V. / Griffin, P.R. / Gati, C. / Nelson, G. / Hunter, M.S. / ...Authors: Zhang, X. / Zhao, F. / Wu, Y. / Yang, J. / Han, G.W. / Zhao, S. / Ishchenko, A. / Ye, L. / Lin, X. / Ding, K. / Dharmarajan, V. / Griffin, P.R. / Gati, C. / Nelson, G. / Hunter, M.S. / Hanson, M.A. / Cherezov, V. / Stevens, R.C. / Tan, W. / Tao, H. / Xu, F.
History
DepositionMar 13, 2017Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Smoothened homolog,Flavodoxin,Smoothened homolog
B: Smoothened homolog,Flavodoxin,Smoothened homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,3667
Polymers145,1532
Non-polymers2,2135
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-5 kcal/mol
Surface area59060 Å2
Unit cell
Length a, b, c (Å)40.590, 349.540, 61.760
Angle α, β, γ (deg.)90.00, 101.10, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

-
Components

#1: Protein Smoothened homolog,Flavodoxin,Smoothened homolog / SMO / Protein Gx


Mass: 72576.586 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 53-433,444-558 / Mutation: E194E, P2A, Y98W
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Smoothened homolog (RESIDUES 53-433), Flavodoxin (RESIDUES 1002-1148), Smoothened homolog (RESIDUES 444-558) and 10 HIS tags
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Desulfovibrio vulgaris (bacteria)
Gene: SMO, SMOH, DVU_2680 / Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Production host: Homo sapiens (human) / References: UniProt: Q99835, UniProt: P00323
#2: Chemical ChemComp-836 / N-methyl-N-[1-[4-(2-methylpyrazol-3-yl)phthalazin-1-yl]piperidin-4-yl]-4-nitro-2-(trifluoromethyl)benzamide


Mass: 539.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24F3N7O3
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Sodium citrate tribasic dihydrate pH 5.0, 36% (v/v) PEG400, 50-200 mM Ammonium nitrate

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 4, 2016 / Details: K-B mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.9→24.9 Å / Num. obs: 37101 / % possible obs: 100 % / Redundancy: 366 % / Biso Wilson estimate: 82.2 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 64.5 % / Rmerge(I) obs: 2.8 / Mean I/σ(I) obs: 0.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C79, 4QIM, 1I1O

4c79

4qim

1i1o


Resolution: 2.9→24.9 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.886 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.34
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1810 4.89 %RANDOM
Rwork0.218 ---
obs0.219 37045 100 %-
Displacement parametersBiso mean: 117.29 Å2
Baniso -1Baniso -2Baniso -3
1-18.2748 Å20 Å2-10.6173 Å2
2--31.6273 Å20 Å2
3----49.9021 Å2
Refine analyzeLuzzati coordinate error obs: 0.76 Å
Refinement stepCycle: 1 / Resolution: 2.9→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9747 0 154 0 9901
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910184HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0313908HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4473SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes207HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1560HARMONIC5
X-RAY DIFFRACTIONt_it10184HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion3.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1307SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11706SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.301 149 5.25 %
Rwork0.28 2689 -
all0.281 2838 -
obs--100 %

+
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