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- PDB-3n1q: Crystal Structure of DhhN bound to CDOFn3 -

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Basic information

Entry
Database: PDB / ID: 3n1q
TitleCrystal Structure of DhhN bound to CDOFn3
Components
  • Cell adhesion molecule-related/down-regulated by oncogenes
  • Desert hedgehog protein
KeywordsPROTEIN BINDING / Binding Sites / Calcium / Cell Adhesion Molecules / Cell Cycle Proteins / Cell Line / Conserved Sequence / Fibronectins / Hedgehog Proteins / Immunoglobulin G / Membrane Glycoproteins / Membrane Proteins / Tertiary / Receptors / Cell Surface / Sequence Homology / Signal Transduction / Tumor Suppressor Proteins
Function / homology
Function and homology information


skeletal muscle satellite cell differentiation / embryonic body morphogenesis / embryonic retina morphogenesis in camera-type eye / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / regulation of steroid biosynthetic process / Ligand-receptor interactions / Transcriptional regulation of testis differentiation / Activation of SMO / patched binding ...skeletal muscle satellite cell differentiation / embryonic body morphogenesis / embryonic retina morphogenesis in camera-type eye / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / regulation of steroid biosynthetic process / Ligand-receptor interactions / Transcriptional regulation of testis differentiation / Activation of SMO / patched binding / positive regulation of skeletal muscle tissue development / Leydig cell differentiation / self proteolysis / male sex determination / Release of Hh-Np from the secreting cell / myoblast fusion / positive regulation of smoothened signaling pathway / positive regulation of small GTPase mediated signal transduction / Class B/2 (Secretin family receptors) / cell fate specification / lens development in camera-type eye / anterior/posterior pattern specification / smoothened signaling pathway / positive regulation of neuroblast proliferation / Myogenesis / protein autoprocessing / spermatid development / neuroblast proliferation / myelination / positive regulation of neuron differentiation / Hedgehog ligand biogenesis / Hedgehog 'on' state / neuron differentiation / cerebral cortex development / cell-cell adhesion / osteoblast differentiation / response to estrogen / cell-cell signaling / response to estradiol / nervous system development / peptidase activity / regulation of gene expression / positive regulation of MAPK cascade / Hydrolases; Acting on ester bonds / cell adhesion / positive regulation of protein phosphorylation / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / positive regulation of transcription by RNA polymerase II / extracellular space / zinc ion binding / plasma membrane
Similarity search - Function
Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Desert hedgehog protein / Cell adhesion molecule-related/down-regulated by oncogenes
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsKavran, J.M. / Leahy, D.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: All mammalian Hedgehog proteins interact with cell adhesion molecule, down-regulated by oncogenes (CDO) and brother of CDO (BOC) in a conserved manner.
Authors: Kavran, J.M. / Ward, M.D. / Oladosu, O.O. / Mulepati, S. / Leahy, D.J.
History
DepositionMay 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Desert hedgehog protein
C: Cell adhesion molecule-related/down-regulated by oncogenes
A: Desert hedgehog protein
D: Cell adhesion molecule-related/down-regulated by oncogenes
E: Desert hedgehog protein
F: Cell adhesion molecule-related/down-regulated by oncogenes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,82015
Polymers92,3836
Non-polymers4379
Water181
1
B: Desert hedgehog protein
C: Cell adhesion molecule-related/down-regulated by oncogenes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9405
Polymers30,7942
Non-polymers1463
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Desert hedgehog protein
D: Cell adhesion molecule-related/down-regulated by oncogenes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9405
Polymers30,7942
Non-polymers1463
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Desert hedgehog protein
F: Cell adhesion molecule-related/down-regulated by oncogenes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9405
Polymers30,7942
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.715, 100.265, 97.260
Angle α, β, γ (deg.)90.00, 98.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Desert hedgehog protein / DHH / HHG-3 / Desert hedgehog protein N-product / Desert hedgehog protein C-product


Mass: 19133.469 Da / Num. of mol.: 3 / Fragment: N-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHH / Production host: Escherichia coli (E. coli) / References: UniProt: O43323
#2: Protein Cell adhesion molecule-related/down-regulated by oncogenes


Mass: 11660.819 Da / Num. of mol.: 3 / Fragment: Third FN3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDON, CDO / Production host: Escherichia coli (E. coli) / References: UniProt: Q4KMG0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 20% peg3350, 200 mM Na(OAc), VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT
DetectorType: RIGAKU SATURN 944+ / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.89→25 Å / Num. obs: 19402

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→22.726 Å / SU ML: 2.18 / σ(F): 0.03 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 895 5.14 %
Rwork0.237 --
obs0.2396 17416 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.001 Å2 / ksol: 0.287 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.3481 Å2-0 Å2-5.1789 Å2
2---11.0669 Å20 Å2
3----10.9192 Å2
Refinement stepCycle: LAST / Resolution: 2.89→22.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5757 0 9 1 5767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035892
X-RAY DIFFRACTIONf_angle_d0.5737974
X-RAY DIFFRACTIONf_dihedral_angle_d14.5672141
X-RAY DIFFRACTIONf_chiral_restr0.037824
X-RAY DIFFRACTIONf_plane_restr0.0041054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.07270.39581060.34571898X-RAY DIFFRACTION62
3.0727-3.30930.31241750.27692838X-RAY DIFFRACTION93
3.3093-3.64110.25791700.24083007X-RAY DIFFRACTION100
3.6411-4.16520.34021410.23212850X-RAY DIFFRACTION92
4.1652-5.23710.22481430.18642875X-RAY DIFFRACTION93
5.2371-22.72690.2121600.18233053X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -19.9498 Å / Origin y: 6.2391 Å / Origin z: -16.8735 Å
111213212223313233
T0.1474 Å20.0089 Å20.0075 Å2-0.1026 Å20.0042 Å2--0.1838 Å2
L0.3052 °20.0107 °2-0.0087 °2-0.1756 °20.1835 °2--0.7055 °2
S-0.0638 Å °0.0291 Å °0.0651 Å °0.0102 Å °0.0121 Å °0.0311 Å °-0.0562 Å °0.0719 Å °-0 Å °
Refinement TLS groupSelection details: all

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