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- PDB-3n1f: Crystal Structure of IhhN bound to CDOFn3 -

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Basic information

Entry
Database: PDB / ID: 3n1f
TitleCrystal Structure of IhhN bound to CDOFn3
Components
  • Cell adhesion molecule-related/down-regulated by oncogenes
  • Indian hedgehog protein
KeywordsPROTEIN BINDING / Binding Sites / 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


vitelline membrane formation / negative regulation of eye pigmentation / camera-type eye photoreceptor cell fate commitment / chondrocyte differentiation involved in endochondral bone morphogenesis / skeletal muscle satellite cell differentiation / embryonic skeletal joint development / embryonic body morphogenesis / embryonic retina morphogenesis in camera-type eye / Formation of lateral plate mesoderm / negative regulation of alpha-beta T cell differentiation ...vitelline membrane formation / negative regulation of eye pigmentation / camera-type eye photoreceptor cell fate commitment / chondrocyte differentiation involved in endochondral bone morphogenesis / skeletal muscle satellite cell differentiation / embryonic skeletal joint development / embryonic body morphogenesis / embryonic retina morphogenesis in camera-type eye / Formation of lateral plate mesoderm / negative regulation of alpha-beta T cell differentiation / embryonic camera-type eye morphogenesis / cholesterol-protein transferase activity / RUNX2 regulates chondrocyte maturation / HHAT G278V doesn't palmitoylate Hh-Np / Ligand-receptor interactions / chondrocyte proliferation / negative regulation of immature T cell proliferation in thymus / negative regulation of T cell differentiation in thymus / positive regulation of T cell differentiation in thymus / epithelial cell-cell adhesion / retinal pigment epithelium development / proteoglycan metabolic process / Activation of SMO / patched binding / embryonic digestive tract morphogenesis / positive regulation of skeletal muscle tissue development / somite development / epithelial cell morphogenesis / self proteolysis / smooth muscle tissue development / Release of Hh-Np from the secreting cell / embryonic pattern specification / head morphogenesis / intein-mediated protein splicing / myoblast fusion / positive regulation of smoothened signaling pathway / pancreas development / positive regulation of small GTPase mediated signal transduction / Class B/2 (Secretin family receptors) / regulation of growth / negative regulation of chondrocyte differentiation / positive regulation of alpha-beta T cell differentiation / cell fate specification / anterior/posterior pattern specification / lens development in camera-type eye / positive regulation of mesenchymal cell proliferation / embryonic digit morphogenesis / smoothened signaling pathway / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / Myogenesis / heart looping / protein autoprocessing / positive regulation of collagen biosynthetic process / neuroblast proliferation / neuron development / bone resorption / maternal process involved in female pregnancy / response to mechanical stimulus / cell maturation / extracellular matrix / positive regulation of neuron differentiation / positive regulation of epithelial cell proliferation / liver regeneration / skeletal system development / Hedgehog ligand biogenesis / Hedgehog 'on' state / multicellular organism growth / cerebral cortex development / cell-cell adhesion / neuron differentiation / osteoblast differentiation / nervous system development / cell-cell signaling / response to estradiol / peptidase activity / regulation of gene expression / in utero embryonic development / Hydrolases; Acting on ester bonds / positive regulation of MAPK cascade / cell adhesion / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / plasma membrane
Similarity search - Function
Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal ...Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / 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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Indian hedgehog protein / Cell adhesion molecule-related/down-regulated by oncogenes
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Indian hedgehog protein
B: Indian hedgehog protein
C: Cell adhesion molecule-related/down-regulated by oncogenes
D: Cell adhesion molecule-related/down-regulated by oncogenes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,93812
Polymers61,5664
Non-polymers3718
Water13,619756
1
A: Indian hedgehog protein
D: Cell adhesion molecule-related/down-regulated by oncogenes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9696
Polymers30,7832
Non-polymers1864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indian hedgehog protein
C: Cell adhesion molecule-related/down-regulated by oncogenes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9696
Polymers30,7832
Non-polymers1864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.758, 98.198, 144.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Indian hedgehog protein / IHH / HHG-2 / Indian hedgehog protein N-product / Indian hedgehog protein C-product


Mass: 19122.406 Da / Num. of mol.: 2 / Fragment: N-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IHH / Production host: Escherichia coli (E. coli) / References: UniProt: Q14623
#2: Protein Cell adhesion molecule-related/down-regulated by oncogenes


Mass: 11660.819 Da / Num. of mol.: 2 / 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.: 2 / 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.: 756 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 20% PEG 3350, 200mM Ca(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: 1.6→100 Å / Num. obs: 67040 / Observed criterion σ(F): 1.45

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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
Starting model: PDB ENTRY 3D1M

3d1m


Resolution: 1.6→25.311 Å / SU ML: 1.39 / σ(F): 0.03 / Stereochemistry target values: ML
Details: Hydrogens were added to the model but not refined as suggested in the Phenix Refinement Program. Reference: Afonine, P.V., Grosse-Kunstleve, R.W. & Adams, P.D. (2005). CCP4 Newsl. 42, contribution 8.
RfactorNum. reflection% reflection
Rfree0.1894 3090 5.05 %
Rwork0.153 --
obs0.1548 61182 90.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.6854 Å2-0 Å2-0 Å2
2---9.1715 Å20 Å2
3----8.6921 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 8 756 4772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097467
X-RAY DIFFRACTIONf_angle_d1.24513165
X-RAY DIFFRACTIONf_dihedral_angle_d14.2971935
X-RAY DIFFRACTIONf_chiral_restr0.085583
X-RAY DIFFRACTIONf_plane_restr0.0051192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62440.25741110.23252175X-RAY DIFFRACTION77
1.6244-1.65110.26231510.20332262X-RAY DIFFRACTION80
1.6511-1.67950.21951460.19572325X-RAY DIFFRACTION82
1.6795-1.71010.25951250.18032403X-RAY DIFFRACTION83
1.7101-1.74290.21271210.16612464X-RAY DIFFRACTION85
1.7429-1.77850.20661400.16532431X-RAY DIFFRACTION85
1.7785-1.81720.23231270.1622511X-RAY DIFFRACTION87
1.8172-1.85940.19121290.16032478X-RAY DIFFRACTION86
1.8594-1.90590.21781140.15222569X-RAY DIFFRACTION88
1.9059-1.95740.2131410.14372625X-RAY DIFFRACTION91
1.9574-2.0150.19671470.1452688X-RAY DIFFRACTION94
2.015-2.080.18291470.14222796X-RAY DIFFRACTION96
2.08-2.15430.16781620.1392785X-RAY DIFFRACTION97
2.1543-2.24050.18011580.1362834X-RAY DIFFRACTION97
2.2405-2.34240.1581480.12992757X-RAY DIFFRACTION96
2.3424-2.46580.18161380.13622754X-RAY DIFFRACTION95
2.4658-2.62020.17611480.13792742X-RAY DIFFRACTION94
2.6202-2.82220.21091470.14952747X-RAY DIFFRACTION94
2.8222-3.10580.19181390.14662800X-RAY DIFFRACTION95
3.1058-3.55420.16581450.13072946X-RAY DIFFRACTION99
3.5542-4.47380.14161450.12562956X-RAY DIFFRACTION99
4.4738-25.31410.17751610.16463044X-RAY DIFFRACTION99

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