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- PDB-4c7a: Crystal structure of the Smoothened CRD, selenomethionine-labeled -

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Basic information

Entry
Database: PDB / ID: 4c7a
TitleCrystal structure of the Smoothened CRD, selenomethionine-labeled
ComponentsSMOOTHENED
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


neural plate morphogenesis / somatic motor neuron differentiation / habenula development / 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 ...neural plate morphogenesis / somatic motor neuron differentiation / habenula development / 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 / BBSome-mediated cargo-targeting to cilium / Activation of SMO / otolith morphogenesis / forebrain dorsal/ventral pattern formation / muscle cell fate commitment / floor plate formation / semicircular canal morphogenesis / diencephalon development / striated muscle cell development / spinal cord motor neuron cell fate specification / arterial endothelial cell fate commitment / embryonic neurocranium morphogenesis / glial cell development / cardioblast differentiation / embryonic camera-type eye development / cerebellum morphogenesis / adenohypophysis development / embryonic viscerocranium morphogenesis / dorsal aorta morphogenesis / spinal cord motor neuron differentiation / endocardial cell differentiation / myofibril assembly / embryonic digestive tract morphogenesis / cardiac ventricle development / somite development / exocrine pancreas development / endocrine pancreas development / hindbrain development / neuron fate commitment / patched binding / smooth muscle tissue development / pattern specification process / telencephalon development / retinal ganglion cell axon guidance / anterior/posterior pattern specification / pancreas development / embryonic pattern specification / positive regulation of smoothened signaling pathway / oxysterol binding / commissural neuron axon guidance / oligodendrocyte development / smoothened signaling pathway / inner ear morphogenesis / cartilage development / forebrain development / neural crest cell differentiation / heart looping / muscle organ development / inner ear development / protein kinase A catalytic subunit binding / receptor clustering / retina development in camera-type eye / negative regulation of protein phosphorylation / vasculogenesis / skeletal muscle fiber development / axon guidance / central nervous system development / protein sequestering activity / G protein-coupled receptor activity / cilium / neuron differentiation / nervous system development / dendrite / plasma membrane
Similarity search - Function
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 ...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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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)44,7986
Polymers44,6642
Non-polymers1344
Water50428
1
A: SMOOTHENED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4203
Polymers22,3321
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SMOOTHENED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3783
Polymers22,3321
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.130, 68.130, 92.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.1554, 0.9274, 0.3402), (0.9488, 0.04429, 0.3128), (0.2751, 0.3714, -0.8868)
Vector: -12.1, -6.139, 53.13)

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Components

#1: Protein SMOOTHENED


Mass: 22331.754 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.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 38.86 % / 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: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→48 Å / Num. obs: 10085 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 26.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 23.7 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 3.9 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→30.47 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.883 / SU B: 22.17 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.533 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28406 483 4.8 %RANDOM
Rwork0.23586 ---
obs0.23803 9576 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.727 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 4 28 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191910
X-RAY DIFFRACTIONr_bond_other_d0.0050.021806
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9762594
X-RAY DIFFRACTIONr_angle_other_deg1.2583.014172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9395232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93524.63482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16615326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0641510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212116
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02414
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6542.728934
X-RAY DIFFRACTIONr_mcbond_other1.6542.725933
X-RAY DIFFRACTIONr_mcangle_it2.5874.0771164
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3863.013976
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 33 -
Rwork0.336 629 -
obs--91.18 %
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)
16.8851-3.5463-1.31072.8710.92482.8032-0.1405-1.00840.43250.19590.2322-0.3023-0.0080.4216-0.09170.0263-0.0178-0.00470.2764-0.02440.0669-4.368-13.47612.12
26.8099-1.567-3.14881.54990.16497.887-0.0019-0.69160.17270.13090.2384-0.37510.51691.568-0.23640.18020.0936-0.00960.4062-0.10.1544-19.502-8.33236.646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 157
2X-RAY DIFFRACTION2B41 - 157

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