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- PDB-4c79: Crystal structure of the Smoothened CRD, native -

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Basic information

Entry
Database: PDB / ID: 4c79
TitleCrystal structure of the Smoothened CRD, native
ComponentsSMOOTHENED
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


somatic motor neuron differentiation / caudal fin morphogenesis / endocrine system development / angioblast cell migration from lateral mesoderm to midline / swim bladder development / swim bladder morphogenesis / neural plate pattern specification / epithelial tube formation / Hedgehog 'off' state / : ...somatic motor neuron differentiation / caudal fin morphogenesis / endocrine system development / angioblast cell migration from lateral mesoderm to midline / swim bladder development / swim bladder morphogenesis / neural plate pattern specification / epithelial tube formation / Hedgehog 'off' state / : / : / neural plate morphogenesis / otolith morphogenesis / floor plate formation / muscle cell fate commitment / semicircular canal morphogenesis / diencephalon development / habenula development / spinal cord motor neuron cell fate specification / forebrain dorsal/ventral pattern formation / arterial endothelial cell fate commitment / striated muscle cell development / cardioblast differentiation / adenohypophysis development / embryonic neurocranium morphogenesis / glial cell development / dorsal aorta morphogenesis / embryonic viscerocranium morphogenesis / myofibril assembly / embryonic camera-type eye development / cardiac ventricle development / endocardial cell differentiation / spinal cord motor neuron differentiation / patched binding / telencephalon development / embryonic digestive tract morphogenesis / somite development / hindbrain development / neuron fate commitment / cerebellum morphogenesis / endocrine pancreas development / smooth muscle tissue development / pattern specification process / oligodendrocyte development / embryonic pattern specification / exocrine pancreas development / commissural neuron axon guidance / oxysterol binding / positive regulation of smoothened signaling pathway / neural crest cell differentiation / pancreas development / retinal ganglion cell axon guidance / cartilage development / muscle organ development / anterior/posterior pattern specification / smoothened signaling pathway / inner ear morphogenesis / heart looping / receptor clustering / protein kinase A catalytic subunit binding / inner ear development / vasculogenesis / skeletal muscle fiber development / forebrain development / protein sequestering activity / negative regulation of protein phosphorylation / central nervous system development / G protein-coupled receptor activity / axon guidance / neuron differentiation / cilium / retina development in camera-type eye / nervous system development / dendrite / plasma membrane
Similarity search - Function
Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Smoothened, transmembrane domain / Smoothened, 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 / Frizzled cysteine-rich domain / Smoothened, transmembrane domain / Smoothened, 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å
AuthorsNachtergaele, S. / Whalen, D.M. / Mydock, L.K. / Zhao, Z. / Malinauskas, T. / Krishnan, K. / Ingham, P.W. / Covey, D.F. / Rohatgi, R. / Siebold, C.
CitationJournal: Elife / Year: 2013
Title: Structure and Function of the Smoothened Extracellular Domain in Vertebrate Hedgehog Signaling
Authors: Nachtergaele, S. / Whalen, D.M. / Mydock, L.K. / Zhao, Z. / Malinauskas, T. / Krishnan, K. / Ingham, P.W. / Covey, D.F. / Siebold, C. / Rohatgi, R.
History
DepositionSep 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMOOTHENED
B: SMOOTHENED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4005
Polymers44,2882
Non-polymers1113
Water86548
1
A: SMOOTHENED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2333
Polymers22,1441
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SMOOTHENED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1672
Polymers22,1441
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.620, 68.620, 95.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 41:157))
211(CHAIN B AND (RESSEQ 41:157))

NCS oper: (Code: given
Matrix: (-0.05527, -0.9494, 0.3092), (-0.9083, -0.08077, -0.4104), (0.4146, -0.3035, -0.8579)
Vector: 0.3091, 2.815, 10.19)

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Components

#1: Protein SMOOTHENED /


Mass: 22144.174 Da / Num. of mol.: 2 / Fragment: CYSTEINE-RICH DOMAIN (CRD), RESIDUES 28-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q90X26
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT CONTAINS ADDITIONAL N-TERMINAL (MA) AND C- TERMINAL (KLEHHHHHH) RESIDUES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.08 % / Description: NONE
Crystal growpH: 7 / Details: 100 MM HEPES PH7.0, PEG 6000 20%, 10 MM ZNCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→31 Å / Num. obs: 7307 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 36.89 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.4
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C7A

4c7a


Resolution: 2.604→29.203 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 340 4.7 %
Rwork0.2136 --
obs0.2157 7275 98.38 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.298 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1-2.0027 Å20 Å20 Å2
2--2.0027 Å20 Å2
3----4.0055 Å2
Refinement stepCycle: LAST / Resolution: 2.604→29.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 3 48 1931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041946
X-RAY DIFFRACTIONf_angle_d0.7142609
X-RAY DIFFRACTIONf_dihedral_angle_d15.71733
X-RAY DIFFRACTIONf_chiral_restr0.049281
X-RAY DIFFRACTIONf_plane_restr0.003338
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A234X-RAY DIFFRACTIONPOSITIONAL
12B234X-RAY DIFFRACTIONPOSITIONAL0.31
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6041-3.28020.27691700.24243360X-RAY DIFFRACTION98
3.2802-29.20470.25181700.20133575X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.96861.6713-0.30051.65920.59330.6286-0.02550.0524-0.17210.13130.0211-0.09030.01910.0432-00.24020.0067-0.0110.16270.0180.2138-14.23383.9941-11.3394
20.4978-0.28620.2311.7810.0041.54060.0344-0.20720.09610.1363-0.1620.09050.2641-0.0976-0.07850.2101-0.0549-0.01820.15780.00930.1824-9.027820.242713.5769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 41:158)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 40:158)

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