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- PDB-8yyz: Crystal structure of Sonic hedgehog in complex with antibody 5E1 ... -

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Basic information

Entry
Database: PDB / ID: 8yyz
TitleCrystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A in the absence of metals
Components
  • Heavy chain antibody 5E1 mutated
  • Light chain antibody 5E1
  • Sonic hedgehog protein N-product
KeywordsIMMUNE SYSTEM / Sonic hedgehog protein (SHH) / antibody / flexible/fluctuated epitope / affinity improvement
Function / homology
Function and homology information


regulation of nodal signaling pathway / positive regulation of skeletal muscle cell proliferation / right lung development / left lung development / primary prostatic bud elongation / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of sclerotome development / tracheoesophageal septum formation / negative regulation of ureter smooth muscle cell differentiation ...regulation of nodal signaling pathway / positive regulation of skeletal muscle cell proliferation / right lung development / left lung development / primary prostatic bud elongation / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of sclerotome development / tracheoesophageal septum formation / negative regulation of ureter smooth muscle cell differentiation / positive regulation of ureter smooth muscle cell differentiation / negative regulation of kidney smooth muscle cell differentiation / positive regulation of kidney smooth muscle cell differentiation / morphogen activity / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / trunk neural crest cell migration / Formation of lateral plate mesoderm / hindgut morphogenesis / polarity specification of anterior/posterior axis / negative regulation of alpha-beta T cell differentiation / regulation of prostatic bud formation / formation of anatomical boundary / positive regulation of striated muscle cell differentiation / regulation of glial cell proliferation / metanephric mesenchymal cell proliferation involved in metanephros development / ventral midline development / trachea morphogenesis / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / telencephalon regionalization / bud outgrowth involved in lung branching / epithelial-mesenchymal cell signaling / Ligand-receptor interactions / lung epithelium development / laminin-1 binding / salivary gland cavitation / negative regulation of cholesterol efflux / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / determination of left/right asymmetry in lateral mesoderm / cell development / spinal cord motor neuron differentiation / negative regulation of T cell differentiation in thymus / establishment of epithelial cell polarity / positive regulation of T cell differentiation in thymus / skeletal muscle cell proliferation / prostate gland development / intermediate filament organization / limb bud formation / embryonic skeletal system development / stem cell development / skeletal muscle fiber differentiation / positive regulation of cerebellar granule cell precursor proliferation / mesenchymal cell apoptotic process / animal organ formation / patched binding / embryonic digestive tract morphogenesis / hindbrain development / positive regulation of skeletal muscle tissue development / somite development / ectoderm development / embryonic foregut morphogenesis / negative regulation of dopaminergic neuron differentiation / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell proliferation involved in lung development / neuron fate commitment / cerebellar granule cell precursor proliferation / Activation of SMO / self proteolysis / positive regulation of immature T cell proliferation in thymus / lung lobe morphogenesis / smooth muscle tissue development / dorsal/ventral neural tube patterning / artery development / lymphoid progenitor cell differentiation / positive regulation of astrocyte differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative thymic T cell selection / regulation of stem cell proliferation / pattern specification process / positive regulation of epithelial cell proliferation involved in prostate gland development / male genitalia development / branching involved in salivary gland morphogenesis / Release of Hh-Np from the secreting cell / epithelial cell proliferation involved in prostate gland development / embryonic pattern specification / lung-associated mesenchyme development / intein-mediated protein splicing / glycosaminoglycan binding / Formation of axial mesoderm / dopaminergic neuron differentiation / metanephros development / thalamus development / Developmental Lineage of Pancreatic Acinar Cells / metanephric collecting duct development / positive thymic T cell selection / camera-type eye development / oligodendrocyte development / positive regulation of smoothened signaling pathway
Similarity search - Function
Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region ...Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily
Similarity search - Domain/homology
IODIDE ION / Sonic hedgehog protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCaaveiro, J.M.M. / Senoo, A. / Kaneda, I. / Tsumoto, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02082, JP18H05425, 16H02420, JP19H05766, JP19H05760, JP20H02531 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121033 Japan
CitationJournal: To Be Published
Title: Biophysical insights to improve affinity of antibodies to fluctuated epitope of antigen: A case of anti-Shh antibody 5E1 against Shh antigen.
Authors: Kaneda, I. / Matsunaga, R. / Nagatoishi, S. / Senoo, A. / Caaveiro, J.M.M. / Kuroda, D. / Tsumoto, K.
History
DepositionApr 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sonic hedgehog protein N-product
H: Heavy chain antibody 5E1 mutated
L: Light chain antibody 5E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,88711
Polymers71,3633
Non-polymers5238
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.510, 84.080, 126.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sonic hedgehog protein N-product / ShhN / Shh N-terminal processed signaling domains / ShhNp


Mass: 19122.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15465

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Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain antibody 5E1 mutated


Mass: 26232.139 Da / Num. of mol.: 1 / Mutation: R102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG / Cell line (production host): EXPI293 / Production host: Homo sapiens (human)
#3: Antibody Light chain antibody 5E1


Mass: 26008.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG / Cell line (production host): EXPI293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 424 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium iodide, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→42.04 Å / Num. obs: 58004 / % possible obs: 98.4 % / Redundancy: 7.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.046 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7699 / CC1/2: 0.851 / Rpim(I) all: 0.23 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.04 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.196 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2218 2422 4.182 %
Rwork0.1844 55499 -
all0.186 --
obs-57921 98.229 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.202 Å20 Å2-0 Å2
2--2.156 Å2-0 Å2
3----0.954 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4483 0 13 416 4912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124630
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164240
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.8176297
X-RAY DIFFRACTIONr_angle_other_deg0.511.7579829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4175585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.221519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22910765
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.58110200
X-RAY DIFFRACTIONr_chiral_restr0.070.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021036
X-RAY DIFFRACTIONr_nbd_refined0.2030.2744
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.23780
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22224
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2336
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1130.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1160.24
X-RAY DIFFRACTIONr_nbd_other0.1550.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.218
X-RAY DIFFRACTIONr_mcbond_it1.3681.5512319
X-RAY DIFFRACTIONr_mcbond_other1.3681.5512319
X-RAY DIFFRACTIONr_mcangle_it2.2792.7762896
X-RAY DIFFRACTIONr_mcangle_other2.2792.7762897
X-RAY DIFFRACTIONr_scbond_it1.7861.7582311
X-RAY DIFFRACTIONr_scbond_other1.7861.7592312
X-RAY DIFFRACTIONr_scangle_it2.9463.1163396
X-RAY DIFFRACTIONr_scangle_other2.9463.1173397
X-RAY DIFFRACTIONr_lrange_it5.48715.9945070
X-RAY DIFFRACTIONr_lrange_other5.36814.9824972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3131520.2583591X-RAY DIFFRACTION86.8647
1.949-2.0030.2381400.2323793X-RAY DIFFRACTION93.8439
2.003-2.060.2551570.2143813X-RAY DIFFRACTION96.9475
2.06-2.1240.2531750.1923701X-RAY DIFFRACTION98.626
2.124-2.1930.221380.1933717X-RAY DIFFRACTION99.7413
2.193-2.270.2341650.1913533X-RAY DIFFRACTION99.9189
2.27-2.3550.2391510.1893444X-RAY DIFFRACTION99.9166
2.355-2.4510.2131570.1733294X-RAY DIFFRACTION99.9421
2.451-2.560.2331470.1873195X-RAY DIFFRACTION100
2.56-2.6840.2391330.1823051X-RAY DIFFRACTION100
2.684-2.8290.2151380.1832905X-RAY DIFFRACTION99.9343
2.829-30.2241080.1662778X-RAY DIFFRACTION99.9307
3-3.2060.2261160.1812606X-RAY DIFFRACTION99.9633
3.206-3.4610.1971230.1772395X-RAY DIFFRACTION99.9603
3.461-3.7880.1871190.1852242X-RAY DIFFRACTION99.9154
3.788-4.2310.214920.1672043X-RAY DIFFRACTION100
4.231-4.8780.188580.1481832X-RAY DIFFRACTION99.8943
4.878-5.9540.249760.181559X-RAY DIFFRACTION99.8778
5.954-8.3370.226460.2241245X-RAY DIFFRACTION99.7682
8.337-42.040.227310.198762X-RAY DIFFRACTION99.8741
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)
14.0919-0.21910.01032.1337-0.67572.03660.02830.0962-0.3089-0.1607-0.02060.10880.1587-0.0099-0.00760.02920.0136-0.00030.01760.00080.0328-1.3108-23.87120.0093
21.0661-0.2325-0.27690.95971.06143.7465-0.0302-0.015-0.138-0.0816-0.10350.0739-0.0756-0.15440.13370.08110.013-0.00910.01740.01460.10940.5194-14.5314-39.3569
30.3530.0231-0.26150.24220.8163.1635-0.09170.0074-0.1244-0.01990.0107-0.00570.12250.08560.08110.1510.05370.01480.08180.01340.119514.4167-27.0231-42.4046
Refinement TLS groupSelection: ALL

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